New England, USA
Would one be permitted to put sticky notes in a book on Shabbat to reference back to those places after Shabbat?
If the plan is to take them out immediately after, yes.
I was concerned about hakhanah, if I then plan on going back and highlighting.
Hakhanah that is just in your mind is not hakhanah. You are marking it now because it is an important passage and you want to return to it. There is nothing that indicates that this is to prepare it so you can underline it.