This is something I read on Snowbums site and tend to paraphrase when people talk manuals:
Whichever manual you use, don't trust the foot pound torque values. Supposedly BMW screwed up some conversions from Newton meters and the aftermarket folks repeated them.
I got my R65 about a year and a half ago and it is my first BMW. It had sat for quite a long time and needed a good amount of work to make it road worthy. The owners manual has a lot of good information for routine maintenance, and the fold-out wiring diagram is really nice to have. Otherwise I've gotten along just fine wit the factory service manual, Snowbum's site, and of course this forum.
The factory manual isn't exactly a friendly piece of literature, but I have found it useful. Haynes and Clymers could probably both be had on the cheap off eBay. If you have any prior experience working on motorycycles I think you'll find the BMW's are, for the most part, pretty easy to understand and work on.
Though the R65 and R45 have a handful of parts that are not shared with their bigger brothers, both sets of bikes are functionally about the same.