There is one direct train from Prague to Cesky Krumlov, leaving Prague daily at 8:02, arriving CK 10:50. The most tricky part will be to get from CK to Salzburg. Train is very slow and at once makes a significant detour between CK and Linz, while after that it is perfectly OK.
Take the bus from Český Krumlov to Linz central train station. Take the train from Linz Hbf to Passau Hbf. Take the train from Passau Hbf to Landshut. Take the train from Landshut to Flughafen München. Fly from Munich (MUC) to Krakow (KRK) 9h 37m. $161 - $499.
From České Budějovic you can get in Český Krumlov by local buses. From Český Krumlov you can go by a bus directly in Prague the same day in the evening. You can also go by bus back to České Budějovice and continue by a train to Prague. Prague and geology: Prague is on intersection of Barrandium and Vltava river. There are no bigger