PKGbackup is mainly just to backup the settings(it will also make a list of tweaks you had installed and reinstall them for you but I find it to be hit or miss). When going from one major release to another(ie iOS5 to iOS6) I always like to start fresh. When you're on iOS6 you can just open Cydia, log into your account and then go to the purchases page to install everything you've paid for. But if you want to save some time, yes PKGBackup will backup everything for you(from SMS, contacts and app settings to a list of tweaks and sources you have in Cydia).