As I said, I may be too stupid to run an Amiga emulator.
I've been using real Amiga's for 25 years and I can't wrap my head around emulators sometimes, either, so it isn't just you. IMHO real hardware makes more sense. But for your first tip, you need a total of six disks (or disk images) to install 3.1. That's Install, Workbench, Locale, Storage, Fonts, and Extras. We can't give you direct links to download these disk images from because "technically" they're still copyrighted, and the copyright police wave a heavy hand on this site sometimes. But a quick Google search for "Amiga Workbench disk images" or the like, should set you right up. From there that will get you a working 3.1, anyway, but you might have better luck downloading a pre-configured hard drive image. I hear AmiKit and the like are good, although again, I don't use emulators so am probably not the best source on a recommendation for those.
http://en.wikipedia.org/wiki/AmiKit