You can save all your game status via a normal backup in iTunes. When iTunes does the backup, it'll save each game state. Then, after an upgrade, you can 'restore from backup" and it'll put the iPad back to the way it was - except you'll be on the more current iOS.
However, I must warn you that there is no jail break for iOS 6 at this time, so if you upgrade to iOS 6.x, you will lose your jail break.
Just so's you know...
Marilyn