A blog post by Tobias Bucknell describes the logistical nuts and bolts of how he writes a novel. Everyone's process will be different, of course, but for him, it begins with slips of paper to capture ideas. Organization and actual writing comes after that. The comments contain some discussion of free software tools that help organize the process of writing a novel, such as Writer's Cafe and CopyWrite. There are many others, of course, some of which are free, some of which aren't.
There are other tools that are just for the getting-text-on-the-page part of writing, minimalist tools like PyRoom and Q10. Another program, Crimson Edit is a pretty minimalist writing environment that let's you have different files/chapters open in the tabs of a single WIP. It appears to be intended primarily as a tool for computer programmers, but it looks like it would serve quite well for novelists. My pals @stoolpigeon and @Shadow_Wrought tipped me off to a couple of these.
I've used Q10 and quite like it. I didn't realize how distracted I actually was by my writing environment. It's much better than the stripped-down MS Word environment that I often use for writing. Interestingly, I find the default orange-on-black color scheme of Q10 serves as a visual cue to my brain to open up and begin actually writing. My usual screen space is black on white, or very colorful and active. The totemic value of this very retro screen is like sinking into the writing mood. This is almost certainly a much better habituation cue than a cigar or a glass of scotch.
All of this makes me reflect on how people organized and wrote books pre-word processor, pre-typewriter and pre-ballpoint pen. It's all the more impressive an effort, and reminds me yet again that good writing arises from the dedication and skill of the writer. Good tools help, but they are only as valuable as the hand that guides them.