I preferred trying to atomize things and it worked for certain types of Notes. I like the fact that it was easy to see what I had by looking in a folder. I also liked that it forced me to come up with short names to describe it. However, that was also the downside because of the limitation of file name length.
I was unable to stick with this system because it did not allow me to relate the ideas very well. I also came to the realization that many of the ideas I thought were atomic were actually ideas that related things together. So I went down the rabbit hole trying to work with properties and tags, etc. I used index Notes or maps of content, but was unable to consistently continue using them as I often would want to reframe things in a different way. So while doing that I never got rid of the old index notes that were framing them originally. I never kept clearing out what was left from the old systems.
I Began Relying heavily on voice recordings that I would transcribe. These would work well because I could relate many ideas together and often in the process of describing them I would come across an interesting twist, and it would be recorded. I would manually transcribe these recordings and sometimes break those out into outlines. But rather than pull ideas or sentences into notes where they were related, I opted to often keep them in place in the vicinity of the semi related ideas that were described during that recording session.
I used template scripts to extract content into other notes, leaving behind the original content as an embed from the note where it gets extracted. But also had it so that in the note where it was extracted to, there is a link back to the block where it was extracted from. Extract to specified heading with Note Composer - #13 by I-d-as
I also experimented with embedding visual notes using Excalidraw Systems like those that Zsolt Viczian shows in his visual thinking workshop. I also used all types of dataview systems, including some wild ones designed by people here on the forum Dataviewjs query that separates 2nd level of nested tags into headers - #5 by holroy
I could go on and on about the many different ways I’ve had organized my notes, and in fact, I believe that this is actually a very helpful process. The hardest part is unraveling all that you’ve created after the fact. It can be very disheartening