Ok, I think I understand.
Are you selecting the books on the iPad? You need to select the books under the Libraries heading in iTunes, towards the top. If you don't see that option, open iTunes Preferences and select Show: Books in the General tab.
You can only change the book title on the iTunes copy, and then sync it to the iPad.
If the books are not actually on the computer, then try right clicking on the iPad and choosing Transfer Purchases. This may or may not put the books in the iTunes library. Books added directly to iBooks by email don't always sync back to the computer.
If they do not transfer back so you can edit them, then delete the books from iBooks on the iPad, then add them to iTunes on the computer first. {You'll need the copy on your computer to do this, so if you deleted it you may have to download it again} Make the changes, and sync back to the iPad.
You'll find your book syncing options under the Books tab at the top of iTunes only when the iPad is plugged in and selected.
Let me know if that helps, or not.
