I break it up into chapters that have 5-20 pages each, each with a major plot split. By each chapter title, I have a little note, like "MP1S1, Fpg;8" - Main Path 1 Section 1, Finished pages; 8. And then I have lots and lots of chapters.
For pages, I put little notes in the title of the page. Such as, (memories), (memories 2), (conversation), (Unfinished/no links), (Focus switch) - those are the basic tags I put on the title, just as little notes to myself. They're all going to be deleted before I publish it of course.