MDSinMI:I can add layouts without a problem, each as chapters.
I'm not sure if you are mixing Quark terms, but a Project is like what other programs call files or documents. Each project can contain one or more Layouts. Layouts are like individual files, but all contained within one project. You can use layouts for a variety of things, like a multiple single-language brochurres. Each layout could have the same graphics and general layout, but you could have a different layout for each language without having different project files. Another could be a business card, letterhead and envelope all in one project.
You probably know that, but from your post, I couldn't tell if your chapters were projects or layouts within a single project.
To make a book, you go to File>New>Book, give it a name, save it somewhere, then add projects to the book as chapters.
MDSinMI:What exactly is the book master page doing if the only thing of use to the actual pages and chapters is their master page?
Where is the "book master" you are talking about? I'm new to version 8, but I don't remember a single master page that controls the whole book. You can syncronize things like styles, lists and colors, but to have the same master pages in all of the chapters, I think you have to do that manually. If you want to change the look of all of the master pages like moving, resizing, adding or removing elements, you could do all of that to the first chapter, select all, copy, then paste-in-place on the master pages of the other chapters.
Also, and this is just for my curiosity, why 50 2-page chapters, instead of fewer chapters with more pages in each?