Avoid taking notes on scraps of paper. The best solution is a meticulously maintained engineering notebook. Write everything down, clearly and concisely. The good sisters of my grammar school all but committed suicide over their failed attempts to teach me penmanship, so such clarity is a particular headache for me. I've learned to slow down and print, since most of the time I can't read my own script.
Some engineers document directly into a computer file.
If your environment is so perfect that you can always seamlessly switch to the editor perhaps this works - if you keep backups. In most cases, though, being stuck in a program you can't exit you are forced to make notes on paper. Use one set of schematics to record changes. This is your master development drawing set. Staple them together and clearly label them as your masters.