When you arrived to the MUC airport, there is a train from Flughafen (airport in German), it runs right from there.
The city center is Main platz. There are two trains that go there. S8 and S1. The fastest is S8. I made a mistake and took S1, it took me 45 minutes to get to the city center. S8 goes straight to the center while S1 goes around the whole city and makes lots of stops.
It cost 10.40 euro for one-time trip from/to Flughafen. If you plan to take more Subway trips that day - buy 11.40 euro all day pass.
Other things about Munich:
Main bus station called Munchen ZOB Hackerbrucke
Address: Arnulfstrasse 21, Munich
---Taking bus to get around Bavaria is often more convenient and much less expensive that trains.
Main train station called Munchen Hbf
is located near bus station (just one stop away on S-bahn).