I've been using MinHub which is (for the moment) an Apple-exclusive app that is very inexpensive but has been a great tool the past couple of years! What do you use to keep track of your youth attendance?
MinistryTracker.Com is has a check-in option but it also an extremely robust CMS. It also allow teens to sign themselves in and print out a name tag on the fly. If you try to fill in out the data, it will become a full-time job so just use the functionality that you need and do not worry about the rest of it.