Not sure if I get the question, but if Munich was just supposed to be your base for going to Füssen you could skip Munich altogether and go to Füssen and overnight there.
If train connections don't suit your requirements keep in mind that all major rental car companies charge no extra fee for one-way rentals within Germany.
The auto route from the Black Forest along Lake Constance to Füssen, and then further East along or through the Alps to Berchtesgaden is very nice and mostly scenic.

Hi cowboy,
your suggestion is utmost helpful.

I have more questions though. Do the rental cars come with gps cause we know nuts about the directions and have not rented any cars before. Do you have any auto companies which we could rent from Gengenbach?

Thanks.

I can tell you for a fact that Europcar is one agency that will either rent you a car equipped with GPS or they will rent you a separate GPS to use in your rental car.

Did this last year for a car rental out of Munich airport (MUC).

As dukey wrote. While GPS costs a bit per day, it will probably still be not that much to bring your own.
Not sure if Gegenbach has a franchise, but if you use location search on the websites of Avis, Sixt, Europcar and Hertz you should at least get some info where the nearest is.
There "should" be an office of all of the above in Berchtesgaden but you need to check that, too.