It's a patchwork, and it changed during the industrial revolution when catholic farmers and agricultural workers from the countryside came into the cities. These days, catholic towns and municipalities in Bavaria get one holiday more than protestant. Since my employer moved offices from a small protestant city to a medium catholic town, I profit from that!

OP; if you decide on a place in Franconia or the Oberpfalz (i.e. the North of the federal state of Bavaria) I can probably find out its religious make-up. For southern Bavaria, go with catholic. Schwaben (the Bavarian part) I'm not sure about.

That said: Catholic is probably the easiest for story purposes.