My opinion:
1. Open empty library in Calibre and drag your Sci Fi folder into it (or some other folder with ca 20-50 books). See what happens. If it's too messy, you can select all, delete from Calibre and repeat with different settings (to tell Calibre if it detects title from file or from file name and how). I have no idea if the regular expression can be made to look at folder name, search the forum.
You can drag in bunch of mobis and epubs and take data from file, in my experience it's pretty successful with those formats.
2. Get few different books in and look for metadata - it helps you to learn what info you consider important and what fields you need to add. For example some time ago I found that I want to know who's the cover artist. People here have some very good ideas about custom columns, I've swiped a few.
It's easy to change 50 books if you decide to have subgenres (Cooking.it, Cooking.fr, etc), with several hundred it's harder. So, don't hurry.
3. In my opinion best format is the original. Calibre will convert, read, export it; but from Calibre it's easyly accessible, you can put your own comments into metadata (like 'awful quality, but best what I can get'). And who knows, maybe by the time you get to reading it you've gotten better quality copy.
Last but not least: Welcome to Mobileread!
