I only have one vault, with subfolders representing subjects. I might have to put subfolders inside subfolders, depending on the situation. This has some pros and cons:
Pros:
- Easy to see a representation in graph view
- Able to switch between notes quickly
- Able to interlink through notes of (almost) unrelated subjects
Cons:
- Hard to navigate
- Planning out folder structure can take quite a long time
My advice is to have a vault for every main subject, and have some (but not too much) subfolders.
I usually write a note for every key topic or new idea. Sometimes, I might piece together multiple sources into one note. I also add table of content notes, although this isn’t that necessary.
This is all how mine notes work, so this may not be optimal. I switched to Obsidian halfway through the creation of my notes vault, so some details weren’t specifically planned. But, I’m satisfied with my result.