Traditional note-taking is flawed. Take a look into Zettelkasten and stop caring about "folder organization". Logseq is great for that. I much prefer it over Obsidian because it's an outliner. Backlinks and tags make note-taking not only a breeze, but fun.

I strongly suggest that you completely ignore methodologies. Write wherever it first seems fit, and keep making backlinks as a way to breadcrumb your way back to your notes. That's how I do it and it has served me extremely well.