We went to both Munich & Salzburg last June with our 11 yr. & 14 yr. children.
In Munich we did RS Walking tour via app, watched the glockenspiel in the Marienplatz, toured the Residenz & Nymphenburg Palace, enjoyed watching the deer while eating/drinking at Hirschgarten, did the BMW plant tour (highly recommend), took day trips to see Herrenchiemsee, went to Mittenwald for the Karwendelbahn and hiked up to Andechs from Herrsching. We walked through the Englisch Garten stopping on 2 separate visits at both the Chinesischer Turm for a bite & the other biergarten along the lake. We also watched the surfers.
In Salzburg we did the Fraulein Maria Sound of Music bike tour (highlight of our stay), explored the city with RS audio tour, went to the Hohensalzburg Fortress and walked along the Monchsberg path ending with lunch at Augustiner.
My children enjoyed both cities. The BMW plant tour & Fraulein Maria Bike tour were the highlights from each city for my kids. There is plenty more to do, see and explore in each location.