I have the left-hand sidebar enabled on the Mac's iTunes (if it's not showing the option-command-S should get it to show), and when I connect a device I select it on that left-hand sidebar :
And then on the left-hand side of the iTunes screen select the Books tab to select and sync ibooks, epubs and/or PDFs :
As long as the book / epub / PDF is in your computer's iTunes library (File > Add To library will add them if they are on your Mac but not in iTunes ; if you have Mavericks on your Mac then you add them via File > Add To Library to the iBooks app on your Mac) then they should show on that tab for syncing.