First question--you convert them to whatever format works best for your ebook reader. If you have an ebookwise (I looked at your profile), you convert to .rb for it.

Official advice is that you never, ever, EVER touch Calibre's database folder & archives; you convert-and-export to somewhere else. Someone who speaks code or database of Calibre's flavor could probably ignore that advice; for the rest of us, Calibre is an interface for changing ebooks from one place to ebooks of a different format (or the same format) somewhere else, and you don't touch its working files at all.