Err.. no bus between Prague to Cesky Krumlov. You'll have to take the train.
See http://www.cd.cz/ (or alternatively the German bahn site) for schedules.
And if you heard all about the fantastic rail system in Europe - unfortunately this does not apply to the Czech Rail system. The ultra cheap rail fares in Czech R. come at a price - old trains that are slow. But they get you were you want to go, so it is possible to use them without too many problems.
And you should book flights from Prague to Split as far in advance as possible. One or two weeks before departure prices will be very high, high enough that the train will be the cheaper option.
Cesky Krumlov is a little rustic spot - corners of it are still the same as they were 20 years ago. Unfortunately it is quite well-known. There are some other towns though that are nice - Karlovy Vary for example. And if you are interested in a trip into Germany take a look at Dresden.
BTW, Cesky Krumlov is quite small. If you come late in the evening I would suggest calling ahead to make sure you have a place to stay. So don't book ahead, but don't just drop in either. You have better things to do (like sightseeing) than to hunt for a hostel bed all over town after you get off the train.