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I guess you have few responses because few people use Macs. I assume the process is similar with a PC.
If you don't use an e-reader, your best best are any sites that sell books without DRM. A lot of smaller publishers, like Baen Books (speculative fiction website) sell such ebooks. Most of these sites will offer ePubs, and either Mobi or AZW. (Calibre can freely convert between these formats, so it doesn't matter which one you get.) You might also be able to get PDFs, but those are painful if you use an e-reader.
iBooks exist, but I don't know if you can get those from a mobile device to your Mac.
It's simple:
1. Download the book. I would have a specialized directory/folder to download the ebooks into.
2. Go into Calibre and upload the book from there. (Calibre will store the books in a separate directory/folder. You can delete the ebooks from the specialized directory/folder afterward.)
3. Tell Calibre to back up your ebooks. You do this by selecting Calibre library, and then export. This will backup all your ebooks, preferably in a different drive (such as a USB key).
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