As a blind person I'm dependent on electronic copies of books so that my screen reading software can read the text aloud for me. Obviously visual highlights etc aren't something I use, but I do want to be able to mark and annotate as and when needed.
As hughlle mentions, Digital Rights Management (DRM) is a real pain in the arse! I usually save a PDF file out as a plain text file, at which point I can add zzz at every chapter heading, so I can quickly navigate through the book by heading by searching for zzz. If I'm reading a novel then I'll add a zzz at the point I finish reading it for the day, so I can jump to the end of the text file and search for zzz with the direction set to up.
If PDF files are not DRM restricted but still have security enabled, then I run it through optical character recognition (OCR) to convert it to a plain text file or Word doc.
Obviously you can use other 'bookmark' combinations as you need, such as xxx as an important revision section or yyy for case studies that you need to know for examinations. The only thing you want to make sure of is to use character combinations that won't be found in regular words, else you'll spend your life trying to track down the point you intended to mark!
I'm hoping to return to university to study for a Masters next year, so I'll probably be doing a lot of this myself!
Hope that helps,
Giles