I'm a mix of Harper and Todd. First book was written in OpenOffice (LibreOffice didn't exist then, now I use it instead of OpenOffice) using Master Document.
Now I write in Scrivener until it's ready for conversion. Export it to odt and open it in LibreOffice for formatting.
After this there will be two tracks. One generates the pdf for CreateSpace. The other goes to Calibre for conversion to epub and mobi, possibly with a side trip into Sigil if I need to edit individual files in epub (embedding a font, adding jpegs, etc). At this stage I have to keep track of my ISBN's since at least in Sweden the requirement is that paper books have a separate ISBN from electronic books. No distinction between epub and mobi, however.
With two separate tracks, the big problem arises with revisions - somebody always finds a missed typo, or an incorrectly formatted chapter title creeps in for unexplained reasons. For revisions I don't go back to Scrivener. I start with the latest odt file, make all the changes necessary and then split it again into the pdf branch and the Calibre branch. It's a good idea to make a checklist the first time you go through the process to make sure nothing is missed.
As far as the creative process is concerned, the part done in Scrivener, I like to have a detailed synopsis, although only once did I do a chapter-by-chapter analysis, when I had a very formal structure to the book, alternating viewpoint between my two protagonists in alternate chapters. I also have very detailed character descriptions, using a template I modified from Elizabeth George's book 'Write Away'. I added extra questions and removed some less important ones. I also write a prehistory of at least my main characters, and I'm now beginning to make similarly detailed descriptions of locations, including drawing maps and building layouts.
Finally I make sure I have a very detailed timeline in LibreOffice Calc (==MS Excel). This allows me to make sure that the pace is not too fast - imagine, say, a woman giving birth in six months - or too slow - a twelve month pregnancy! In one case I used this to calculate the ages in years and months of the characters at each event. This was important, for several characters were in their teens, where a month or two can make a big difference - taking driving test, buying alcohol, etc.
All these working documents - and more - I can store in Scrivener, where I usually use a separate subdocument for each chapter, although if there is a crucial scene that I want to keep separate for some reason (eg writing it out of turn in order to document it), I have a subdocument for that, too, even if it isn't a full chapter when I write it. It will become one later.
In Scrivener you have different sections to your project. In one you have the book, with, as I say, chapters as subdocuments, and in another you have working papers, where I have access to all the things I've mentioned above. I can flip between these documents at will, and when I come back to the chapter I'm working on, I'm at the place I was at when I left it, of course.
Scrivener was originally a Mac product but now they've made a Windows version, and I believe it works under Wine on linux.
But don't listen to me. I'm a wannabe.
