How would I go about setting up spreads and all? Make a document the size
of the two pages together? And then indicate a fold line?
Yup. Make the artboard big enough to include spreads with trim marks. You can just drag-copy a set of the vertical lines from trim marks to the center (aligning to a guide) using the direct selection tool in order to indicate the fold line. Note that trim marks are not the same things as crop marks.
Assuming a straight saddle-stitched self-cover (with no elaborate multifolds), you'll end up with eight Illustrator files: pgs. 16 and 1 will be on one document, 2 and 3 on another, and so on.
Talk to your printer. More likely than not, they'll take your eight Illustrator files and drop them into Quark for film output.
Too bad your company won't spring for a page layout program. Even if they never produce another multipage brochure -- and especially given your familiarity with Quark and InDesign -- it's false economy.
=-= Harron =-=