I have a single system that I use for both digital and paper notes. Start writing, put new stuff at the end. Date every entry. Use topic headings that stand out clearly from the text. When it gets too full, slap a date on the file / notebook and open a new one. Mostly this is not for returning to, but for thinking things through, although the paper system is also good for to do lists.
Btw, try out those translucent sticky notes for the highlights.