Open up your first chapter and start highlighting, when you do so a little bubble pops up on the right and you can make a note.

Don't start changing things chapter by chapter right away, do every chapter like this and then go back and see what you've got.

Adding onto this- color-code your highlights. Orange for questionable/contradictory plotlines, yellow for sentences that need re-wording, green for things you like, blue for things that need expansion... It really forces you to re-read carefully and establishes a process for editing. I'm slogging through a project written in multiple NaNoWriMo sessions and it's made it infinitely easier to follow a 'what needs to be fixed in this section' route.