Clay Moore posts a quick little description of a way to approach writing your fiction.
What i am proposing is not that you throw out the Chapter system at all. Rather I want you to think of your story as a collection of scenes, as if you were playing out the movie of your story in your head. Each scene can then be completely mapped out. You know who are in the scene, and the goal is for each character in that scene. You get all the pre-think done, and then do the writing. I find that my characters are better behaved.
This scene technique has worked wonders with my own writing. When I have a complicated plot, this technique helps with keeping the plots straight.
Another benefit to this scene based system is that I can see where I am lacking in the book. A character may suddenly appear and I need a scene to introduce that character.
This approach is very similar to how I write my comics.