Very good pick, Ken. The hotel is only about 75 yds (down the street) from the Moosach S-Bahn station, which is about 30 minutes from the airport and less than 20 minutes to Marienplatz. If the OP gets a Gesamtnetz Gruppen Tageskarte, for 24,30€, at the airport, it will cover any and all conveyances of the Munich metro (MVV) for up to 30 hours, from midnight (AM) to 6 AM the following morning. That could include from the airport to Moosach Bhf, then RT from Moosach to downtown Munich, and Moosach back to the airport. Hopefully, one day of the check-in period for the hotel, 3 PM to 11 AM, will cover their stopover in Munich. When does the layover begin and end?
The OP should be aware that the S-Bahn from Moosach to the airport splits at Neufahrn, with the front half of the train going to Freising and the back half going to the airport. Look for signs on the cars giving their final destination.