ThunderRoad,
I like Scrivener for writing but I wouldn't use it to layout a book. Scrivener is a great program but it isn't a layout program, it is a writing program. For layout, I'd use InDesign or Quark Xpress and that is what most professional publishers would use as well (some might have an old copy of Framemaker but it is unlikely because it is so old). From my experience, most authors just write the book using their favorite word processing program (sadly it is often Word) and then when it is time to publish it, they give the publisher (or a designer) the file and they take that file and import it into a layout program and design the look and layout of the book (the font size, line spacing, etc). Putting a book together is rather complicated, especially if you aren't used to doing it. Most of the time it is left to professionals. Most designers are familiar with gutter, bleed, footnotes, etc. But there are more complicated things that you have to know about when you put a book together. Things like creep, imposition, not to mention how to calculate the thickness of the spine based on the number of pages and the weight of the paper that is going to be used (not easy to do if you aren't used to it). Normally the printer will take care of the creep and impose the pages but in some cases you need to be aware of it when you are designing the book.
If you are making it more for yourself, you wouldn't need to worry so much about creep but depending on the thickness, it might make it hard to read the pages in the middle. Imposition will be easier because you aren't using an actual printing press (it won't be easy but it will be easier). One thing that is tough if you make it yourself is binding it. Stapling or glueing are options but if I were you, I take it somewhere to be done. It is more expensive but the results will be much better.
Best of luck,
Mecha
