I have begun to think of the novel as the marathon of the writing world, and it certainly involves a lot of planning. Some people work through this with scores of post-it notes and writing on their windows and walls ala Good Will Hunting, but it seems like a lot of people work through it using trial and error. One computer programmer has tried to improve the situation by coming up with an organizing software package. This free download helps you organize your book by scene as opposed to chapter, in order to help you map out what you are doing and rearrange things as needed. The gentleman developer has a whole site devoted to this, and you can look at that and watch his explanatory video here:
I think it’s definitely worth checking out.