if your using Rock, u should have created a user id and password so that the JB apps save everytime u open Rock and next time u restore and JB, all u need to do is log into Rock with the username/ password and restore all your JB apps because they will be saved to your username
There is no way to backup Cydia apps to iTunes unless you're talking about using the Cydia app PkgBackup, which saves your backup as a contact and thus syncs with iTunes.
iTunes does not recognize the jailbreak, nor any of the apps you install from Cydia or Rock.