Welcome to MobileRead, Ylurien!
I'd tend to reluctantly agree that for what you're wanting to do, the PDF approach is the better one to try first (normally I avoid, and recommend avoiding them like the plague). You can find a "Best Known Method" for making PDFs for the Reader here
. Hope that helps.
If not, come on back, there's a lot of expertise here and I'm sure we can help you work out what you need to do.