How do I backup App Store purchased apps on a jailbroken iPhone?

My iPhone has been JB for a while now, but I'm not sure how I'm supposed to go about backing up the apps so I won't lose my game progress and whatnot. Can you still backup apps through iTunes like a non-JB iOS device, or does that method no longer work?

I plan on going back to a non-JB iOS device eventually (thanks to iOS7 fixing a few of the issues I had with the OS), and I didn't want to lose anything.

Thanks!