Hi kelly,
First, you will never go "into" the city of Munich. The airport is about 20 miles NE of Munich. It's all highway (if you want it to be) right from the airport to Innsbruck. We haven't done this trip in the dark but have done so many trips on secondary roads at night without any troubles.
Buy a "Vignette" (highway toll sticker) for driving on the highways in Austria. A 10 day sticker is 7.80 Euro. You can buy them at any "rest stop", gas station, convenience store, etc. along the way.
Our absolute favorite place in the Innsbruck area is the Gasthof Badl in Hall in Tirol. We stayed here in '01, '03 and '05. It's just 15 minutes from Innsbruck and very easy on/off the highway. Very friendly hosts, buffet breakfast, nice restaurant and great views of the Alps (ask for a room w/balcony). Plus, we love the old town of Hall in Tirol itself.
www.badl.at
Another great town/village to stay in is Mittenwald, Germany, which is 45 minutes from Innsbruck. We stayed twice at the Pension Schwalbennestl in Mittenwald.
www.schwalbennestl.de
We have photo's of these places at:
www.worldisround.com/home/pja1/travel15.html
Hope this helps.
Paul