Ignorance hurts. How do I know this? Until a few days ago I'd been using iTunes to transfer books from my laptop to my iPad, where I use the awesome (and free!) Marvin to read e-books. I use Calibre to manage my library on my laptop, I have a separate folder for each book in my Calibre library, and it's a real pain in the neck if I want to move a bunch of things to my iPad at once using iTunes. Or, rather, it was. I finally got sick of doing that, and a little Google-ing turned up the wonderful Calibre native driver for Marvin, which lets Calibre and Marvin talk directly to one another.
This is something I seem to keep re-learning: if a routine computing task seems really diffcult then you're probably doing it wrong.