At times I've just stopped taking notes because of the high activation energy required, now I just work with my Tablet or Notepad and worry about organising or integrating into my knowledge graph later.
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.
By the way, I was pleasantly surprised to find out that Logseq is open source! That's a fantastic bonus. Thanks again for pointing me in this direction – it's making a real difference for me.