I've also found that taking notes is extremely helpful when I'm trying to understand something. Especially when I'm reading on the computer, where it's so easy to open a new tab and do something different. However, every time I've tried to use something like OneNote or org-mode, or anything that I think will help me organize my notes, I get extremely frustrated. So, instead, I just keep a cheap spiral bound notebook next to my computer. Being forced to write on something other than the computer is great, and I've found I don't need to organize the notes really, they're in chronological order and easy to flip through.
I keep what is essentially a lab logbook next my work desk. The natural chronological order works mostly well: (1) notes on related topics are often close in time (the temporal locality, in a way) and (2) it helps to find "stuff I was working on two months ago", or "right after I finished that project in May".
Also, I noticed I prefer writing on separate sheets better than a notebook. This way I can take several sheets from different time periods and work with them as a single group. When I am done, sorting them back is easy as long as each sheet is marked with the day it was originally worked on.
