Just to add, you have a direct train to Regensburg from the train station under the MUC Central Area between T2 and T1 (you know this probably already).

If you end up in NUE, you just take the underground to the main station and from there either a regional train or you check on the bahn.de website for a cheap advance ticket for a ICE train (every 2 hours). Both regional and ICE train have about the same travel time. You will have a train every hour to Regensburg.