For the beginning I tend to just do a list of what major events are to occur in the story (If and when) This is done during the general story outline process.
Then I just write out the story passages and then put a little asterisk by each choice that I haven’t written out yet. I tend to “section off” certain passages from each other to signify the different major branches. I tend to keep the potential for confusion to a minimum by writing a entire path from beginning to end and then going back to finish off the minor branches before starting on another major path.
I tend to separate the major paths themselves into different Word documents so it doesn’t get too overwhelming to scroll through. Though I often find myself doing a lot of page scrolling anyway!
Finally I keep track of all the choices and paths I haven’t worked on yet on a separate “notes” document, which eliminates any possibility of me missing a choice I need to finish up.