I know I can take the train from Munich to Garmisch with the Bayern Ticket. And I know I can use the Bayern to get to Salzburg. But is the best way to get from Garmisch to Salzburg going back to Munich or taking the train from Garmisch to Innsbruck and on to Salzburg. And is that route covered by the Bayern? Any help is appreciated!
I think you would be best off going back to Munich. That segment is by regional train and would be covered by the Bayern-Ticket. Then take a train to Salzburg. As long as the trip from Munich to Salzburg is by regional trains, it would also be covered by the Bayern-Ticket. As for going through Innsbruck, the Bayern-Ticket would get you to Mittenwald. The next stop after Mittenwald is Scharnitz, in Austria, so you would need a point-point ticket from Mittenwald to Innsbruck. From Innsbruck, probably the fastest way is down the Inn to Kufstein with an Austrian Rail ticket, and from there by German trains, which would be covered by the Bayern-Ticket, via Rosenheim, to Salzburg. A 2nd class Bahn ticket from Mittenwald to Innsbruck would cost €11,10/adult. An Austrian Rail ticket from Innsbruck to Kufstein would cost €13,90/adult in 2nd class. Using regional trains from Innsbruck to Kufstein would make the trip from Garmisch to Salzburg about an hour longer. I took the train from Mittenwald to Seefeld, the high point of the route to Innsbruck, and it was very pretty, but from Innsbruck down to Kufstein (Brannenburg, actually, and it's almost to Rosenheim) is nothing special. From Rosenheim to Salzburg is the same route either way.