Since you will see many sites on your tour, I would recommend just enjoying the ambiance of Munich. Sit, relax, have a beer.
And places to do that (some noted previously):
Viktualienmarkt - stroll the outdoor shops, sit, have a brat and beer
Englischer Garden - stroll the beautiful gardens, enjoy nature in the city. Make sure you watch the surfers in the river at the start of the park. Sit, have a beer from Fräulein Grüneis.
Go to a beer garden, sit have a beer, enjoy the ambiance (notice a trend?) - Alter Botanischer Garten is a nice park with a nice beer garden
For dinner, I like the Augustiner-Keller beer garden. Just you, your family and 3000 of your closest new friends.

As noted upthread, I would pick a hotel near the train station, easy access to the airport. The Aloft and Meridian are nice.