There are several questions in here, most of which are difficult to answer without knowing a bit more about how you're approaching your particular project.
First, are you writing the entire book first, before you query and write your proposal? If that's the case, remember that for non-fiction writers, you DON'T have to have the entire book written first. You pitch a proposal first, which is its own unique creature. (And, of course, you've got to query agents first to get them interested in reading your proposal. Don't forget THAT step.)
Assuming you're taking the Traditional Publishing Route, then worrying about documentation and the formatting of your pictures and sources in your manuscript is putting the cart so far before the horse it's in the next county. You'll want to concentrate on putting together your proposal first -- and as veinglory said, sources and their formatting probably wouldn't matter when it comes to the platform, though I'd guess you might want to list some of your sources in the section where you discuss similar or related works. (For tips on nonfiction proposals, there are several threads here in AW, as well as books like The Idiot's Guide to Getting Published, which takes you through a proposal section by section.)
Eventually, you'll likely need a few sample chapters to submit (if your proposal sparks interest, publishers will ask for two or three chapters). At that point, in my experience, I've found the Chicago Manual of Style to be a fairly good template for formatting your citations and sources---and for purposes of citing sources in sample chapters, that's what I would use. Once your book sells to a publisher, however, the publisher generally will TELL you their preferences or in house style for citing your sources and documentation.
Finally, as far as "how much documentation" to use, I try to endnote and document as much as I can. I find a lack of endnotes in non-fiction to be rather off-putting, but that's just me.
(Apologies if I haven't actually answered your question!)