I made the mistake of using my personal app store account when setting up my school's computers. Of course, there didn't seem to be a choice... now that I've done that, how do I permit the users of each of the computers to use their own app store accounts to run updates?
I would just sign out of your account and set up the correct account on each Mac. Open the App Store and see what updates are available. Any admin user can run normal updates and then you can see what purchases (if any) are on the wrong account.
You may have dodged a bullet if only system updates were done as they don't get tied as a permanent purchase. Even so, the cloning process means only one Mac registered for the iLife suite and you can wait for advice from Apple if that decision can be reversed if you'll just use one of the other accounts to update two machines going forward.
Ask a second question or edit this with more details once you've tried this on one test Mac to see what else needs fixing.