Without going through the hassle of creating a choice tree, you can just use notes on another document to keep track of your story.
Write down all your major events and when they're supposed to take place in the story. Add new ones (or delete discarded ideas) when necessary.
Keep track of all the choices you aren't currently writing about in your notes, delete them whenever you get back to them. Also mark the choice you haven't gotten to yet with an asterisk in the actual text and then delete the asterisk when you finally get around to writing for that choice.
It's a simple way of keeping track of which choices you have and haven't worked on.