I too have my own preferences. What I've figured out about myself is that I like to flip between "practice" materials and "archival". Practice notes are more l

I too have my own preferences. What I've figured out about myself is that I like to flip between "practice" materials and "archival". Practice notes are more like your preferences: 70-pager subject notebooks, pencil or ballpoint, clips and manila folders. Those are better for drawing in, because they are thin enough and transparent enough to trace through, and therefore you can refine a doodle into a more developed illustration without leaving the notebook. To go smaller, index cards are very portable and stay rigid enough to work outdoors on improvised surfaces. Those are what I like when I want to build up quick reference. The "archival" materials are art projects: if you've really developed an idea, make it beautiful. This can be 80% tracing off the practice notes through a graphite transfer. Or it can go straight to digital/typed. I don't aim for linked systems of notes at all. What I've found is that either I copy it all into the one place I need, or I don't need it. The copying is the important part. Once that's done, it's been "loaded" in my head as well, and I can move on.