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.
Your best bet is to not upgrade to iOS 6.X for now, if you want to preserve your jailbreak, unless you have an iPad 1. In that case, feel free to update, since iOS 5.1.1 is the latest version of iOS that can be installed on the iPad 1.When an iOS 6 jailbreak is released, it will be announced in the official iOS jailbreak thread. Subscribe to it and keep an eye on it. http://www.ipadforums.net/ipad-hacking/89458-official-ios6-jailbreak-status-thread.html