I don't see why you can't check in before you leave the states. The only trick is that AB only lets you check in via your booking code and name. I'm not 100% positive with AB, but the booking code you got from UA (6 digits) is usually not the same one as in the other carrier's database. The good news in that AB has a US toll free number you can call at any time. They should be able to give you the AB booking code, and with that you will be able to check in up to 30 hours before your flight - plenty of time before your MUC flight. To repeat - if you either do this or checkin in at MUC, be sure to show them your baggage receipts so they can enter the bags into their system.

Assuming the return is the same - you should check since I'm not sure AB will interline bags to UA - many low-cost carriers don't interline.