it hides all of your cyida packages in a list that backs up with itunes backup, then after restore it will use that list to query and download everything from cydia again. I believe it stores any personalized settings from the cydia apps in the aforementioned itunes backup
i used pkgbackup, it saves all of your cydia packages as a contact, then you backup your phone in itunes, restore your phone, then restore from backup. next re-jailbreak your phone and reinstall pkgbackup then load your old packages up
Aptbackup does not restore settings. Nothing can do that yet for some reason. Chronus used to do it but the dev abandoned Chronus. Pkgbackup is the best for reinstalling all your installed cydia packages but it doesn't do settings.