The reason iBooks can't be syncd via iTunes, is because iBooks has its own App.
To Sync across Devices then:
Open the iBooks app.
Select iBooks > Preferences > General.
Select "Sync bookmarks, highlights and collections across devices."
Now it gets a little different, if you have ePub books bought/downloaded from places other than iBooks Store.
You will need a App that connect to iPad via WebDAV or by Server. Thinks like GoodReader, FileApp Pro or UDB Disk Apps in the App Store. You upload to them, and then "Open In"~ iBooks from the Share menu . . This can also be achieved with Dropbox, Google Drive, One Drive and the likes.