IBooks storing books in iFile not with original file names but renamed to 16 length Hex character

Calibre is one of the best open source eBook Management tools:

http://calibre-ebook.com/

Features include:

• Library Management
• E-book conversion
• Syncing to e-book reader devices
• Downloading news from the web and converting it into e-book form
• Comprehensive e-book viewer
• Content server for online access to your book collection

You might not be happy with the current functionality of iTunes, but here's how to works. The folder structure from iBooks in iOS doesn't get reflected in iTunes, so you can't control which category new books will arrive in on the device.

You can have a folder of epub files and drag them into iTunes, but they go where iTunes puts them, not a folder of your choosing. This allows bulk injection of hundreds or thousands of books into management for syncing.

The computer version of iTunes will then make a copy of those files in it's Media folder and sync them to all iOS devices the next time they sync (assuming you have the sync rules to sync all Books to each device).

Now, the good news is that if you go ahead and file a book in a category on your iOS device other than Books, that information does sync back to iTunes and the next sync will re-organize things on other devices so you file once, and then sync each device to get them all in sync.

Furthermore, if you have a new iOS device (or erase an existing device) and push all books to that device. The folder status from the last device sync goes to that empty iBooks on iOS.

If and when Apple adds a control to iTunes, you may be able to order books on iTunes just like you can order App icons in iTunes and then sync the device to see the results.