The iPad’s iBooks application supports the standard ePub format as well as books you purchase through the iBooks store. This means that you can use the huge library of free eBooks available from Project Gutenberg & Google Books. You can also read eBooks purchased through other sources such as The Pragmatic Bookshelf. Simply drag any ePub books you download to iTunes and after you sync your iPad, those books will appear in iBooks.
Does not sync my books.
this is all not workinnnnnnnnn
Or get bookman for your ipad and you can ftp any ebook, cbr or pdf to your ipad.
It might not sync through iTunes, but just email it to yourself, open the email on your iOS device, then choose the book and tap "Open in iBooks".