the best advice i found on organising a novel came from carolyn see's book on writing, which is something like "advice to writers and other dreamers." i always forget the title.
at first, she says, you read your entire MS and make notes on what you have and what you need to have. something like:
I have: p.2 Shirley meets Bill.
I need : Who's Bill?
I have: p. 5 Shirley gets drunk in Florida
I need: How did she get there?
after you are done with this, and fixed all your holes, you physically arrange your novel on some large surface, in little piles of chapters or scenes, and re-arrange if necessary.
so if your MS is not typed up yet, maybe the first step is to type all of it. let it sit for a couple of weeks. read it, and without making any corrections, make all the notes (what you have, what you need). then fix whatever needs fixing.
check her book out, i found it extremely helpful, funny, and encouraging.