The Simplest, Most Practical Heptabase Note-Taking Method #2 | Building Deep Knowledge Connections: A Three-Stage Note Organization Method

Hello everyone, I'm Arch (assignarch). I work as a project manager coach, and I'm also a PhD candidate at the National Taiwan University of Science and Technology (NTUST), Graduate Institute of Applied Science and Technology, in the Science Education and Digital Learning division. My research focus is "project management education."

As a PM wearing many hats, I rely heavily on note-taking tools to learn and organize knowledge.

After years of using Evernote and Notion, I started exploring Heptabase.

I've now been a paying user for two years, and I can honestly say Heptabase has exceeded my expectations.

Through constant iteration on how I take notes, I've built my own workflow in Heptabase — one I use for writing, course design, classroom learning, reading, and developing professional knowledge.

In this series on Heptabase note-taking, I'll walk you through how to apply this approach and workflow to build your own knowledge system.

I split my Heptabase note-taking method into two parts:

How to Take a Good Note
Building Deep Knowledge Connections (this article)

This is part #2: Building Deep Knowledge Connections.

This note organization method is about turning the notes you've already built into a knowledge system that lasts. We'll do this through Heptabase's three core features: Card, Section, and Whiteboard.

What Is a Deep Knowledge Connection?

A deep knowledge connection means the "new knowledge" forms enough associations with the "knowledge already in your head" that you can extrapolate from one example to many.

"Depth" here doesn't mean how advanced your understanding of the subject matter is — it means how tightly your existing knowledge is linked to your new knowledge.

When people learn something new and can immediately apply it across different situations, that's deep learning at work.

How deep you need to go depends on what you want to do with the new knowledge:

An engineer learning to write > can produce technical specification documents
A project manager learning to code > can communicate better with engineers
A homemaker learning home repair > can take better care of their living space

Take the recent generative AI hype as an example:

I use AI to design the mechanics and content of educational games, making my games more refined and rigorous.

Combining AI with my professional expertise reflects a deeper grasp of AI as a tool. By contrast, if I only used AI to chat or look up trivia, I'd just be replacing Google.

The other key point about depth: it has to connect to your existing experience and how you actually use it.

Flip it around: if the knowledge or skill you're learning has zero connection to your environment or work, you'll forget it fast.

Years ago, I picked up a bit of Japanese because I wanted to speak it on a trip to Japan. But I don't watch Japanese dramas, I don't watch anime, and there's nothing in my daily life that requires Japanese. So before long, I'd forgotten almost everything.

Why Build Knowledge Connections When Taking Notes?

The more connections, the deeper the knowledge, and the longer the memory lasts.

The things we learn best are usually the things tied to our daily lives — they generate the most connections.

For example, a good game designer has to think about:

Player input habits
The game's visual interface
The game's setting and worldbuilding
The pacing of the storyline
The emotional projection onto characters

Each one is its own discipline. The more tightly these areas are integrated in your head, the more things you can "naturally take into account" when designing a game.

The more closely a new piece of knowledge connects with what you already know, the more easily you grow.

Take a project manager:

If you know the tech, you can answer client technical questions directly without going back to the engineering team
If you know how to negotiate, you can work out trade-offs with clients to land more deals
If you understand product management and the market, you can prioritize software features properly

Building deep knowledge is the ultimate goal of note-taking. Note-taking is the method.

When organizing my Heptabase notes, I follow three principles for building deep knowledge:

Knowledge has to be managed before it can be properly understood and applied.
The more abstract or massive the concept or system, the more it needs to be broken down into smaller pieces.
You need to grasp and oversee the entire architecture (The Big Picture), not just look at individual cards.

How Do You Build Deep Knowledge Connections?

In the previous article we talked about How to Take a Good Note.

The focus of this chapter is: assuming you already have notes, how do you "organize" them?

My method splits into three stages:

Revise & Dissect: Break complex knowledge into smaller, more digestible units, so each concept can be retrieved and recombined independently.
Label & Connect: Use color, bold, and lines to give knowledge meaning, so key points are easy to spot and concepts can be linked.
Categorize & Organize: Use Heptabase's Sections and Whiteboards to build a knowledge structure — a personal knowledge map you can keep growing over time.

These methods are not mutually exclusive. Treat them as a mindset (just keep them in mind).

In practice, I jump between them constantly, adapting to what I'm learning and what I need at the moment.

1. Revise & Dissect

This stage is about breaking concepts apart.

We need to isolate each concept inside a piece of knowledge and give it a complete explanation of its own.

Below is a screenshot from my notes on Buy Back Your Time:

Left: my reading notes from the original text
Right: the standalone concepts I extracted from it

If a concept feels easy to you, don't force yourself to dissect it. For example, domain-specific knowledge is often common sense to people in that field.

Engineers already know the difference between variables and constants. But for a student just starting to code, that distinction probably needs its own note.

The paraphrasing we discussed in the previous chapter also gets used during dissection.

A small note on paraphrasing:

In some specific cases, I'll keep the original wording entirely intact — papers, quotations, and so on. The reason is that future me might need to cite the original text directly.

Dissection in Heptabase looks like:

Splitting one card into multiple cards
Each card holding only one concept
Pulling examples of a concept out into their own cards

The benefit:

You understand each concept better, and you can quickly find the practical examples that go with it.

Here's a screenshot from when I was designing a course and broke the "Design Thinking" process into multiple cards:

Each step of design thinking is one card
Each example for that step is one card
Each piece of relevant research for that step is one card

2. Label & Connect

This stage is about assigning meaning.

Labeling and connecting are the keys to deep understanding.

Whether you're labeling or linking, the underlying move is the same: you're attaching meaning to knowledge — and that meaning is your understanding of it.

2.1 Use color and formatting to mark text

Inside a card, I usually use color to highlight what matters — key concepts and numbers.

Different colors can stand for different levels of importance or different categories, helping you scan and recognize quickly.

I personally prefer a clean style, so I only use one color.

Another common form of marking is bold. Pair it with color and you get a two-layer highlight.

Here's a screenshot from my academic research notes, where I've colored and bolded "the parts I think matter":

2.2 Use color to mark whole cards

Once you've fully dissected a topic into multiple cards, you might want to color the important ones.

In Heptabase, I usually color processes, classic case studies, and important theories with different colors so I can spot the key cards at a glance.

The screenshot below is from my writing notes. The yellow card is my "creative process" — Ideation, Writing, Editing, Finalizing, Image Production, Social Media Formatting, and Call to Action (CTA).

When I'm stuck on a piece of writing, I come back to this process to figure out where I'm blocked, run through the writing thinking again, and usually find a new angle to break through.

2.3 Use lines to express relationships between cards

I rarely use lines when organizing notes, but a lot of people love using them to map relationships between concepts.

I usually only use lines when designing lesson plans, where the goal is to make the structure crystal clear.

Below is a note from when I was designing a "Design Thinking" course and used lines to show relationships.

Honestly, I don't really like the line feature — when there are too many lines, the whole note becomes a mess, especially when you try to move cards around.

I hate clutter, so I'd rather use Sections to group things and rarely use lines.

You'll notice that when I use Heptabase, the focus is on how a feature gets used and how it serves you.

Note-taking is deeply personal. Everyone has different habits, and you'll need to spend some time finding what works best for you.

My method is just a reference. What matters is what the method is for.

Remember, don't take notes just to take notes.

Bold, color, lines — they're all techniques to help build connections inside your own head.

In the act of marking, we usually absorb the meaning of the marks subconsciously. But if you're just doing it to do it, or doing it for fun (just because you want pretty-looking notes), it's hard to actually learn anything.

3. Categorize & Organize

This stage is about architecture.

For organizing, I use Heptabase's Sections and Whiteboards.

The goal is to build a clear knowledge map, helping us systematically understand what we know.

Below is my Writing Knowledge Map.

3.1 The basic structure of categorizing and organizing

A knowledge map needs at least two layers.

For the first layer, I use Whiteboards to separate completely different topics:

Entrepreneurship: equity design, employee handbook, hiring, product development, market analysis, marketing
Academic: literature review, theories, research methods, research processes, classic schools of thought
Writing: SEO, short-form writing, positioning across different social platforms, copy templates
Work logs: office culture, leave processes, common knowledge
Course design: contains multiple Whiteboards, one per course

If you're already used to taking notes, you'll usually have 3 or more layers.

The screenshot below shows all of my Whiteboards — currently around 4 layers.

The role of a Whiteboard:

Lets you see your knowledge system at a glance
Insulates you from unrelated knowledge
Lets you focus on the system you're working in

For the second layer, I use Sections to group cards that share a topic but cover different angles.

Take Academic, my biggest current note cluster, as an example:

Research methods: surveys, interviews, content analysis of digital learning behavior
Learning theories: situated learning, scaffolding theory, flow theory, cognitive load theory, PBL
Domain knowledge: Kanban, project management education, game-based learning
Class notes: weekly notes, assignments, exam highlights, grading weights, professor office hours

Below is my Academic Whiteboard. There are some scattered cards, but three larger Sections:

Game-based Learning
Project Management
Games in Project Management

Looking at how Sections are organized, you'll notice "Games in Project Management" is something I deliberately broke out. Game-based learning and project management are both fairly mainstream research areas, but games in project management is relatively niche — so it deserves a deeper, more focused space.

Sections here serve to:

Categorize based on your understanding of the knowledge
Categorize based on what the knowledge means to you
Continuously refine your mental model of the knowledge

You probably already get this: knowledge shifts based on your goals. The way I categorize things is built around making it easier to do specific kinds of research.

3.2 Your knowledge map is an organic system

Your knowledge map is an organic system, and it grows over time.

This is probably the most important sentence in this article. Keywords: organic, grows.

Because my academic research is huge, my Whiteboards have many layers.

You can see in the screenshot below that my Academic Whiteboard is slowly expanding...

When I take a class, I open a Whiteboard for that class
When a topic accumulates too many notes, I open a Whiteboard for that topic
When a Whiteboard starts to look messy, that's the signal to re-categorize and reorganize

This screenshot is the same Whiteboard as the previous one. There are actually a lot of uncategorized cards — they're important to my learning, but not yet "important enough to need categorizing."

Treat your Whiteboards as the knowledge map of your second brain. Knowledge keeps adding up:

When I take a class, I record the lecture
After class, I clean up the notes — dissecting and labeling
Once that's done, I file the new cards into the existing Whiteboard structure

PS: I also keep the original lecture transcripts so I can come back to them later.

How Do You Internalize the Three-Stage Method into a Daily Habit?

Methods are just references. What matters is repeated practice, finding the way that fits you:

Learn to assign meaning to new knowledge
Build the muscle of dissecting and connecting knowledge
Develop your own pattern of learning and thinking

This is a continuous optimization process.

Everyone's knowledge system is unique. The point is finding what works for you.

One last thing: don't be a perfectionist, and don't waste time making things look pretty.

My notes are actually pretty messy — just like my thoughts — because I'm learning a lot and barely have time to clean up. But if a piece of knowledge really matters, I'll make the time to organize it, because organizing is part of the learning.

Same line as before: don't take notes just to take notes.

That's the entire mindset behind how I organize notes. The three stages aren't a rigid process — they're a tool for letting scattered cards grow into a knowledge map. Pick the messiest Whiteboard you have right now, and start dissecting it today.

FAQ

Q: Do I have to follow the three stages in order? A: No. The three stages are a mindset, not a process. In practice, I jump between them — halfway through dissecting I might realize I need to re-categorize, or while categorizing I might dissect a card further. That happens all the time.

Q: Do I have to use the Link feature in Heptabase? A: Not necessarily. I rarely use lines myself, because too many of them clutter the Whiteboard and make moving cards messier. I'd rather use Sections to categorize. I only use lines for scenarios like designing lesson plans, where I need to express a process.

Q: How many layers should my knowledge map (Whiteboard) have? A: At least two — first layer using Whiteboards to separate topics (e.g., entrepreneurship, academic, writing), second layer using Sections to separate angles within a topic. If a topic gets large, it'll naturally grow to 3+ layers. There's no fixed rule on how many layers you should have — it's entirely down to how you want to manage your knowledge.

Q: My notes keep piling up and the Whiteboard looks messy. What should I do? A: That's the signal to re-categorize and reorganize. Group similar cards into a new Section, or open a new Whiteboard for a sub-topic that's grown too big. The knowledge map is an organic system — it's supposed to grow.