Vienna to Prague with stop in Cesky Krumlov

Check on shuttles. There are several that operate from cities like Salzburg, Vienna, etc to Cesky Krumlov. From CK to Prague you could also use a shuttle or there is a bus that is convenient and a bit cheaper than the shuttles - but the shuttles are quite inexpensive themselves. I took the shuttle from Salzburg to CK and then the next day I took a bus from CK to Prague but I could also have scheduled a shuttle if the bus hadn't been available or convenient. Much much cheaper than a rental car.

My wife and I did what you are planning. We used CK Shuttle, and were very satisfied with the service. Our overnight was in the Penzion Krumlov, which we also liked a lot (nice room, good breakfast). We ate at a really good restaurant by the river whose name I can't remember, but it was recommended "for Americans" by the woman at the counter at the Penzion. We thought Cesky Krumlov was wonderful.

And you can get a shuttle to pick you up at your Vienna hotel and drop you at your CK hotel, then do the same the next day, dropping off in Prague.

Another vote for CK Shuttle. It was easy, affordable, and the door-to-door drop-off was a nice perk.