As for remembering what places need working on, just add something to the start of the title of each of those pages; eg. [NEEDS WORK].
For the actual branching, I would recommend planning your story out before writing, making sure to include enough choices to keep it interesting and nonlinear. If there's one part of the story that seems too linear, try adding more choices where you can. For example, say in the middle of a long page, a suspicious person forces you to get into their car. But what if I don't want to get in the car? There's a new choice. Make 2 new pages, one for getting in the car and one for not getting in. You could end up making a whole side branch from a choice that wasn't originally even included!
Also, don't overuse death pages. Stories that are mainly do-or-die choices (and therefore extremely linear) get unpublished for low ratings 90% of the time. The impact of a death isn't that great when I've had to reset after 7 of them!
Note: It's okay to make a story with an overall linear plot IF said plot is long enough with enough choices and side branches. My most recent story is a straight line of 13 chapters, but there's choices thrown in that although not affecting the overall outcome, add a bit more variety to the storygame. There's even a few choices that determine which character you get to play through the plot with!
Anyway, good luck in making less linear, more enjoyable storygames!
