Efficiently organize 100s of externally stored ebooks within iBooks for iPad without doing it manually in collections? I have hundreds of ebooks stored on an external drive of mine. I don't want them on my MacBook Pro because I don't want them taking up space due to the fact that I don't read ebooks on my Mac. I just bought the new iPad so I can read these books.

In iTunes, I tried creating folders to put the books into in an attempt to organize them properly but they all just appear in the same huge list within the iBooks app on the iPad and I have to manually create collections and put the books in there.

Surely there has to be a better and more efficient way of doing this? I have tried Googling all over no question is specific to mine with a viable solution.

Basically to summarize:


I have all my iBooks on an external drive which I want to sync with my iPad but without having them stored on my computer. What is the best way to go about this?
How can I keep my collection organized so when I sync, I don't have to keep searching for new books I added to manually add them to an existing or new collection?
Managing ebooks with iTunes is a horrific experience for the user.  If you are willing to adjust your expectations, Calibre does a good job, but it lacks polish.  You may find it doesn't work the way you expect, but with some patience you may find it does what you want (and more!)