You can also use iCloud for all the games which support it. Typically I only upgrade from a jailbroken iOS to another jailbroken iOS and use app backup in Cydia.
I strongly recommend that before you upgrade, install appbackup and backup all your games. Then copy the folder of backups to your computer. That way, when the iOS 7 jailbreak comes out, you can install AppBackup, copy that folder from your computer to your jailbroken iOS 7 iPad, and restore all the game saves 100% back to their current state. I've lost game saves with iCloud and iTunes backups. Not sure why that happened but regardless, AppBackup is a 100% foolproof method of backing up game saves and restoring them on a new iOS. The catch is, it's only available in Cydia.
I have a link to step by step instructions if you would like. This way you'll guarantee you won't lose a single game save. You can also backup any other App Store app if you want. Just let me know and I'll post the link. I can't recommend AppBackup enough. It's one of my favorite things about jailbreaking. I have game saves from around 2010.