I originally started out using a single highlighter to make it easier to find the various Views/Details and ended up highlighting almost everything with it's own color.
I use yellow for AN470 (non-flush) rivets, orange for AN426 (flush) rivets, purple for views/details, green for instructions (drill this, enlarge this, etc), blue for notes (to make sure I see it!), and pink for any hardware (bolts, screws, etc).
Distinguishing the types of rivets is very important for me, as I will be much less likely to forget to countersink/dimple for flush rivets.. now I can see at a glance if there are any orange marks and if so, what piece they are on.
Here's an example:
I use yellow for AN470 (non-flush) rivets, orange for AN426 (flush) rivets, purple for views/details, green for instructions (drill this, enlarge this, etc), blue for notes (to make sure I see it!), and pink for any hardware (bolts, screws, etc).
Distinguishing the types of rivets is very important for me, as I will be much less likely to forget to countersink/dimple for flush rivets.. now I can see at a glance if there are any orange marks and if so, what piece they are on.
Here's an example: