When the next iOS update comes out, what happens to my jailbreak? If I upgrade the iOS and then later get the new jailbreak (If that's how it works) will I lose all my jailbreak apps? Or will they come back?
If you update you will lose the jailbreak and you will have to wait until they release a new jailbreak for the new firmware. There are several Cydia apps you can use to backup your installations(xBackup, PKGBackup and APTBackup to name a few).