I have only written one story here, and it was for a contest so I was under time constraints. I haven't made anything so big that I needed to keep track of it. Mostly what I did was copy my pages to word and tried to keep them in order over there. I don't know how well the chapters work, so I don't know if they're a viable option.
As for 'fake' choices, to me it depends on the content of those choices. Sometimes they lead to entertaining little side pockets of information or humor or drama. That's a pretty good use. Sometimes they let you go backwards to an older path, which is also pretty good. I generally only really get annoyed if you give someone four choices, and three of them end up with the exact same outcome with the exact same description of that outcome. Pretty much, whenever there is a 'choice' there should be something different, for each one, or at least a 'bridge' to another part of the story. I've been satisfied with a 'fake' choice with even one or two lines of difference.
Pretty much, people want to think that what they click makes a difference.