Where to stay in Bavaria?

We lived in Augsburg, 50 miles west of Munich for four years and spent lots of time in the Garmish area. Also, did Salzburg/Berchtesgaden. I suggest with 5-6 days that you can visit both, you should not try to do day trips from one to the other.
Spend more time in the Garmish area. However, Salzburg is great, but do the Eagle's Nest in Berchtesgaden if you can.

While in Garmisch, recommend going up to the Zugspitze as well as seeing the castles.

Keep in mind that next year (2020) is the once-in-a-decade Oberammergau Passion Play, so that area of Bavaria (which is close to Garmisch-Partenkirchen) will probably be exceptionally crowded.

geovagriffith, thank you for the info. max, I just read in this forum about the passion play next summer. I’ll have to change plans. Would Berchtesgaden and Salzburg be affected with the crowds for the passion play? I will research Chamonix and maybe head to that direction. Our trip ends in Zurich, so it might be good to stay nearby.

I'll assume you will have a car? Schönau am Königssee is a good summer location. I stayed at Unterartenreitlehen years ago before they renovated. Minimal seven day stay I'm afraid though now. Within walking distance of restaurants, the Jennerbahn and Königssee. There are many FEWO/Holiday apartments in Schönau am Königssee, but I would book early to get the better local. München and Garmisch-Partenkirchen and Mittenwald are a two to two and a half hour drive away unfortunately, but Salzburg is only a 40 minutes drive away. I like to use P+R Salzburg Süd in Salzburg.

http://www.unterartenreit.de/
https://www.ramsau.de/webcam-malerwinkel.html
https://www.foto-webcam.eu/webcam/funtenseetauern/

I've never been to Chamonix-Mont-Blanc, but it's on my "Visit" list.

mchpp, I'm not sure if we'll have a car just yet. I will have to see what our final plans end up being. Thanks for the info. about Salzburg and Schönau am Königssee.

With children that age I'd look further north. Base out of Nuremberg and you have Rothenburg, Dinklesbuhl, and Nordlingen right there. Also the open air museum at Bad Windsheim (which is great for kids). You'd also have the bike paths of Erlangen, the castles in Nuremberg, Wurzburg, Hohenau, and Colmburg, and the open market, train and toy museum's in Nuremberg itself.

Frankonia is beautiful in the summer.

If you want mountains and less city/town stuff look at the Oztal region in Tirol. From Kitzbuhl to Obergurgle there's a number of small towns that cater to skiing in the winter but have great hiking in the summer months.

KGC, thank you for the suggestions! I will look into these places. So many wonderful and beautiful places in Europe! It's hard to decide what part to go to.