I agree that your trip into Munich should start with Marienplatz. Besides the Rathaus and it's 11 AM Glockenspiel, nearby is the Frauenkirche (the church with the two rounded domes). You can tour the inside. Additionally, when you are in Marienplatz facing the Rathaus, look behind you, over your right shoulder, and you will see the church tower of St. Peters. For a few Euro, you can climb to the top of the tower for a great view of Marienplatz, Munich, and, on a clear day, the Alps.
There are two S-Bahn lines (S1 & S8) from the airport into Marienplatz. They run alternately every 10 minutes. It doesn't really matter which one you take. S1 takes about 9 minutes longer, but if it is the next one leaving, it gets there 1 minute sooner than the S8.
On the way back, the two S-Bahns leave from different levels in the Marienplatz station. It's best to take the S8, since the S1 often splits in Neufahrn, and only the back half goes to the airport. Pick the station level that says to Ostbahnhof.