How far, and how long is the trip from Cesky Krumlov to Vienna?
You can go to viamichelin.com to get distances and approximate driving times between any two cities in Europe.
http://www.viamichelin.com/tpl/hme/MaHomePage.htm http://maps.google.com/ Those two links are all you need for directions, distance, etc. Driving in rural areas is absolutely no different than in the US, except the signs look different. I cannot stress this enough; You do not want to have a car in ANY European city larger than 500,000 people or so. It is not worth the hassle to park, or pay for parking, or pay congestion fees. And you would be insane to think you will use it to drive from one tourist attraction to another within the city. You can do that in the US, with some effort. You will NOT be able to do that in Europe. There is a reason they have fantastic public transit systems.
You need to check to see if you can take a rental car from CZ to Austria. I don't believe you can take one from Germany to CZ. I would suggest you take a train.
Hertz & no doubt most other rental companies will let you take a car from CZ to Austria and from Germany to CZ. The thing to be aware of is that the drop fees are hefty - as much as a few hundred euros - if you don't return the car to your point of origin.
We haven't been to Cesky, but drove from Vienna to Prague almost 10 years ago - no issue going into CZ - though there are some other central Europe countries that may not work as well. Just best to check with the specific car rental company - and be sure to be very specific (I got a generic response from Budget in Greece and had to re-send the email and say "so I CAN take the car across the border" to which they responded "No". )
I think CZ is pretty mainstream these days. It would be a nice drive - plan for a nice long day along the river (though you can go a more northern route) and up to Cesky. I think it's actually only about 4 hours from Vienna to Salzburg if you went straight through - but I'd just enjoy the drive - stop in Melk if you haven't been there, etc. - lots of cute towns along the Danube.