Although your decision to fly into Munich and out of Cologne makes sense, given the weather conditions in November, much of what makes the Rhine and Mosel areas of Germany charming in late spring, summer, and early fall, is pretty well gone by November. Add to that the short hours of daylight and it may be smarter to spend the entire time in Bavaria, centered in Munich or the immediate environs, exploring Munich and day-tripping to other nearby sights. By staying in Bavaria you could explore not only Munich but the sights to the south: the Royal Castles, Oberammergau, Linderhof (Ludwig's hunting lodge), Garmisch (the Zugspitze), a day trip to Salzburg, a day trip to Rotheburg ob der Tauber. If you're locked in to a Cologne departure, then I would suggest Munich, side trip to the the Royal Castles, Rothenburg, Heidelberg, a drive along the Rhine (stop at any of the wine villages along the way (Ruedesheim, St. Goar, Bacharach - pick one, although most will be pretty well shuttered), and Cologne. While all of this is easily do-able using public transportation, and with apologies to Lee, my preference is to get a rental car, especially during periods when daylight is precious. It simply provides more flexibility. Driving in Germany is pretty much like driving here in the States. I can't really advise you concerning places to stay because I generally try to rent a house or apartment in a village centrally located to the things I want to see and do. Regardless of what you do, have a great time.