I think on the iPad's iBooks, if we purchase an ebook, then in another iPhone, iPad, or iPod Touch, then that ebook is automatically downloaded into our bookshelf.
However, what if it is a .epub or .pdf purchased, say, from O'Reilly? Sometimes the ebook is $29.99 on iBooks store but $25.99 on O'Reilly. It seems that the book won't be automatically downloaded to the bookshelf, but we can use Dropbox or Box.net to transfer to iBooks, and all the highlighting and added notes will be there on each device (sync'ed).
But is there a way to automatically download all books to our library? Otherwise if we have 12 books we kind of have to manage 12 books in each of our device.