When I initially read your question, I thought you wanted to see parts of Munich, Austria, and Switzerland in 6 days, but on re-reading it, I'm not sure. Are you spending time in Austria before Munich, 6 days in Munich, and then time in Switzerland after Munich (or vice versa)?
If you only have 6 days for it all, then you won't have enough time. Munich itself warrants 3-5 days. To get to Switzerland from Munich will consume half a day (6 hours to Zürich) on a train each way (assuming you have to return to Munich).
I would recommend 3 nights in Munich; 1 or 2 nights in Salzburg, and the remaining time either in the Berchtesgaden area of Germany or the Salzkammergut region of Austria (Bad Ischl, Hallstatt, Gmunden).
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