The need for systems for knowledge organization

This is an excerpt from the book "How to Read a Paragraph" which highlights that ideas belong to particular systems (domains such as psychology, sociology etc.) and thinking in terms of systems (with a look to big picture at least).
This is something I experience in myself too. Zettelkasten is so atomic note oriented that even though you connect things and only create notes as branches, and not allow any orphans; it becomes messy in my head.
I wonder what you think about such a top-down structure (in our heads or in our systems, doesn't matter). And I wonder your experiences about remembering what's in your ZK. Did you train yourself to think in terms of building blocks? How do you handle not having an anchor in head?
Selen. Psychology freak.
“You cannot buy the revolution. You cannot make the revolution. You can only be the revolution. It is in your spirit, or it is nowhere.”
― Ursula K. Le Guin
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A quote from an upcoming article on Long Thinking (Cal Newport's term) and the Zettelkasten Method:
The process would be:
In practice, you can't distinguish the two. So, you build a couple of systems, then build the general system, build another specific system and then modify the general system, etc.
I am a Zettler
The article seems interesting, and so does Cal's concept.
Is this podcast episode a right entry point?
It sounds like both a way to structure the Zettelkasten's internal network and a metacognitive process that should run in the mind.
I suggest everyone read "How to Read a Paragraph" to understand your toolbox idea better, by the way. (Though I have a hunch that it's a common reading and I'm behind!)
Selen. Psychology freak.
“You cannot buy the revolution. You cannot make the revolution. You can only be the revolution. It is in your spirit, or it is nowhere.”
― Ursula K. Le Guin
To speak of systems implies the existence of subsystems, and so even within one system there are degrees of generality. The trick is to recognize the degree of generality and write your notes to suit.
Knowledge is organized or structured, usually in many ways at once. If your notes do not reflect your own structure to some degree, they won't be congruent to your thinking and understanding. So your notes - let's not get into the meaning of "atomic" for now - will work best if they reflect the level of organization you are thinking about or understand. Of course, when you don't know a field very well you can't do that effectively.
Let's say you are working on history of some kind. You can be interested, say, the life and times of Henry VIII. There are facts about his various marriages. So you write some notes about them. Then you start thinking about how and why marriages have been made in Western European kingdoms and how Henry's marriages do or do not fit some pattern that you have identified. So you find information and write some cards about that.
Then you get an idea about the nature of royal marriages affecting the incidence of warfare and start to look into that. So you write some notes about this larger idea. By this time you will probably have internalized quite a lot of the history you have gotten interested in, and your reading and thinking will have moved into more general regions of historical study. At each stage you are writing notes that fit the degree of generality of your study, and hopefully your links, keywords, outline structure and terms, etc. - whatever methods you use - will come to reflect your broadening understanding.
If you want top-down, go through a library's catalog and see if you can find something you know about. Chances are that you will eventually do so, and you will feel that their cataloging system doesn't seem very natural to you. At a minimum it would take a long time to learn, and it can't adjust as your own understanding develops.
If you can use them effectively, your linking, keywords (especially compound keywords), outline structure if you use one, names of structure cards, all those things will come to form what is called a "subject language", and to quote Svenonius, "the subject language becomes an analog of knowledge itself". That is, knowledge as you understand it, personal to you.
Oh, I don't know that you want to know in my case... I have weak episodic memory and I look to my ZK to help remind me.