What follows are some brief (and perhaps not very helpful) thoughts from a guy whose writing and publishing resume in magicdom is quite humble indeed. But the wording of your question prompted the reply.
You asked about ... getting a manuscript from the home computer to the bookshelves. Thats what I had to worry about because I was the writer, photographer, designer, editor, publisher and marketer of my book. But given the direction in which you seem to be heading, it sounds like maybe your only real worries should be writing a strong book and, if you think you need one, selecting an agent. Not that those two tasks are easy by any stretch, but being able to focus on them almost exclusively should greatly simplify the process.
It may be that the breadth of your question simply reflects the way you go about educating yourself, i.e., youre thirst for knowledge is omnivorous and so you want to learn everything about a process. But if your discussions with this agent have you thinking that how she markets the book to potential publishers, and how in turn a publisher would market the book to the general public, are important matters for you to learn about and manage (or hire somebody to manage), that would raise a caution flag for me. As we all know, magic is a niche market even in its own niche! So in order for a magicians biography Im assuming thats what youve written to get picked up by a general trade publisher, my guess is that biography had better sell itself.
Just my .02. Whatever you decide to do, Chris, good luck with your project! And if it doesnt work out with the big guys, at least you know there are several quality magic publishers that you could consider. At least in the little world of magic, there is always room for a good biography.