[ldolse]

Actually you use Calibre as a black box, but you let it become the owner of all your files. It's not quite as black box as something like iTunes though.

Like iTunes you need to abide by Calibre's naming conventions, which bothers some users, but I don't have a problem with it personally.

Unlike iTunes you may often find you need to go touch the files directly, primarily when converting from one format to another. Calibre makes that pretty easy to do though, any time you're looking at a book in Calibre you can just right click and ask it to open the directory for that book, the 'o' keyboard shortcut will do this as well. So I manage my metadata in Calibre, but when I'm format shifting to epub I'll often open up the files and tweak the output manually. If you're always content with what Calibre does automatically when format shifting then you may not have much reason to access the files directly.

If you try to keep all your files duplicated elsewhere you're just going to have management headaches. What you can do before you import all the books is try to clean up the filenames a bit to make them as uniform as possible. Then import using the filename regular expression to populate the metadata.