What if your goal is to explore major sights in Czech Republic and also visit Budapest.
- The best method to explore Czech Republic and countries near is for sure to rent a car. As for Example Cesky Krumlov is not on major roads and as you have already noticed good connection is only to Prague. So, there is no night train from Cesky Krumlov.
- So I’d say you need to spend one day (better by car) exploring Cesky Krumlov and Hluboka nad Vlatavou and return to Prague and then do a trip from Prague to Budapest.
Classical route from Prague to Budapest is the following:
Prague -> Brno (at least half a day in Brno)
Brno -> Vienna (at least 2-3 days in Vienna)
Vienna -> Budapest
If you need to return to Prague you should take Budapest -> Bratislava (3-4 hours in Bratislava is enough) and then Bratislava -> Prague.
As for trains… there is a night direct train from Prague to Budapest, living 0:05, arriving 8:35 (schedule cd.cz cost 500 Kč one way. You could try to buy ticket online at cd.cz eShop.
Paying road fees
One important thing: if you travel in Austria, Czech Republic, Slovakia and Hungary you will need to pay for the road when you enter, but it is easy to miss points where you need to stop and pay, so if you decide go by car use instructions here.
Transporation
As for transportation methods: I think Cesky Krumlov and Hluboka is better by car; As for Prague -> Brno -> Viena or Prague -> Brno -> Budapest is better to do this route by bus (studentagency is the best with WIFI, WC, tea or coffee), as driving for a long distance is not cost effective.
