For maps, I highlight important info, make notes in the margins. I try to minimize writing on the maps, except for my routes of intended travel, notated with the magnetic compass courses, adjusted for Variation.

For Nautical Charts, I do the above listed items but, I also use a green highlighter to mark all water that is too shallow for my vessel.

For Aviation Charts, I will sometimes connect the electrical towers, thus showing where the electrical lines are actually running.