Re: Transferring iBooks to iCloud
If you purchased the books from the iBookstore (via iTunes, or iBooks on an iOS device), they're already "in" iCloud. There is no "transfer" option. If you purchased this way, you can safely delete from your iPad and re-download again in the future. If you have iOS 6, you will see a cloud icon by book covers of those not actually on the iPad - and you can just download by clicking the book cover.
If you didn't purchase them via iTunes, but have added ePub or PDF books manually, you will need a backup of them to have access later if you delete from the iPad. I store tons of PDFs and other ePub books not purchased via iTunes on my iPad, spread among many collections, and I do weekly backups to my Mac to ensure they're all preserved. I've been using highlighting, notes and bookmarks extensively, as I'm using large ePub files as part of a post-graduate program. I've done extensive work to organize my collections, and would hate to lose it all. Doing this local backup will also restore them all properly if I get a new device or have to wipe my iPad. This also prevents me from losing a purchased book if it goes "out of print" on the iBookstore. So far as I can tell, an iCloud backup of your iOS device does not backup your non-iTunes purchased books (ePub or PDF). You'd need a local computer backup to iTunes for that.
See here for more details: iBooks: Tips for managing your iBooks library and storage on iOS devices