How to Return to iTunes (and Calibre)?

Like an idiot, I launched iBooks on my Mac after installing Mavericks. All of my books that were in iTunes were transferred to iBooks. Then I realized that I lost a huge amount of metadata and that it was going to be much more difficult to manually transfer books to my iOS devices.

Let me add that I never really trusted Apple and my master database of epub and Amazon books and large pdf's is in the open-source Calibre app. I highly recommend it. It's a good reading app as well. I can't believe how stupid I was.

Anyway, I'm going to reload all of my books from Calibre back into iTunes and fix all of the metadata. I've deleted all of my books from iBooks and deleted its preference file. Do I need to do anything else to keep iBooks from sucking my books out of iTunes again. I do not plan to launch iBooks again until I've read that all of its problems have been fixed.

Thanks.

Update: I can't seem to import ebooks back into iTunes now that I've used iBooks. Does anyone know what I have to undo in order to use iTunes for books again?