There is much to see in both cities (Munich and Salzburg), especially if you like music, so, for your first trip, I would suggest three days in each. Perhaps after this experience, you will change it next time. Three days is not so long for either one.
I think it is silly to rent a car. The train ride is about 1.5 hours and costs (with discount) as little as €19 (each way) if you buy your tickets in enough time. If you like a challenge, try booking your ticket from the German web site in German (
http://www.bahn.de/p/view/buchung/fa..._buchung.shtml).
The German railroad has many price offers (
http://www.bahn.de/p/view/angebot/an...bkanal_020=1#3) and, again if you buy your ticket in advance enough, the prices may even be cheaper than a rail pass, especially if you buy the US one.
Good luck.