So my daughter and I are flying into Munich next March (the 9th) and flying back to Us from Prague on 03/18. Between Munich and Prague, we want to go to Salzburg and Cesky Krumlov during our trip. My question is....would we be best taking a train to Salzburg (overnight) and back to Munich, then take train from Munich to Prague, then go to Cesky Krumlov as a day trip from Prague. Or, would it be easier to go from Munich to Salzburg, to Cesky to Prague?

Go to www.bahn.de/en - German Railways schedule page for all European trains and put in the variations and see which is best.

I think it would be Munich to Salzburg
Salzburg via Linz to Cesky Krumlov
and then to Prague.

Are you staying overnight in Cesky Krumlov?

You can use the bargain Bavarian Ticket Munich to Salzburg - both for about 30-35 euros totals if you use regional trains - about 45 minutes slower than the faster trains -just buy that in Munich station day of travel.

For lots on trains check www.seat61.com; www.budgeteuropetravel.com and www.ricksteves.com.

Munich to Salzburg:

www.bahn.de/en

Choose between express trains from €19 no refunds no changes, or buying a Bayern Ticket on the day for €25 or so and using the Meridian regional trains (shown as M on bahn.de/en)

Salzburg to Prague:

You need to book this at Czech Railways www.cd.cz from €19, you print your own ticket. Plenty of journeys with one easy change at Linz.

You can then do CK as a day trip, also booked at www.cd.cz - see https://www.seat61.com/places-of-int...ky-krumlov.htm

But as the Linz-Prague train passes through Ceske Budejovice (formerly Budweis, where the name of the beer comes from) you might want to go Salzburg-CB-CK, booking Salzburg to CK at www.cd.cz, then book CK to Prague at www.cd.cz or buy on the day.