If you turn off apps to back up will it mess them up when u do a back up

It should not "mess them up" by not including them in the backup. The backup only include the app's data (i.e., position within a game, etc.) and not the app itself. When you restore from a backup, the actual music and apps you purchased will get downloaded again. So, if you need to restore your device and haven't included it in the backup, the only thing you will loose is any information within the app (it will start like a fresh copy). On second thought, if you call that "messed up" then the answer is yes.