For my ATPL exams (completed about 18 months ago) I made sure I understood everything by the end of each week. As a matter of practice I would never be more than 2 weeks out of date with my notes. Notes were kept to a bare minimum. If it was something I understood, I didn't make notes on it. If it was a single fact or equation, I'd note it down and do an example. Each chapter of notes (e.g. VOR or grid nav or thunderstorms) was kept to 2 sides of A4 maximum. This made sure I understood everything, and the facts and figures were easily accessible. I could revise an entire exam in 15 minutes with these notes. By the end of the course (all 14 subjects) my notes could fit into a single A4 folder (a small one!) Too many notes = overload!
The above study made sure I understood stuff for real. The Bristol online question bank made sure I passed all exams first time with 95% average!