We managed to fit both cities/areas into our trip and we're glad we did. With its crowds and tacky souvenir shops, Prague has sort of a Niagara Falls feel to it, but it is a very beautiful city and not that difficult to find quiet niches away from the circus. I loved Cesky Krumlov but cycling there from Prague was frustrating. The Czech Republic boasts of over 4000km of bike paths. No doubt it's true but they're not necessarily well-marked nor is it easy to figure out which are suited to long-distance touring and which are technical mountain bike trails. Plus, it's very hilly.
Cycling from Salzburg through the Salzkammergut was enjoyable. The Austrian cycling routes are sign-posted and well-mapped, including surface conditions, elevation and traffic. The rainy weather might have kept some of the crowds away, but aside from the glut of Mozart shops, I didn't find Salzburg to be touristy.
We spent a similar amount of time in both places. For me, it was enought time in Prague/Cesky Krumlov but I want to see more of Salzburg and the lakes district. Hopefully in better weather so I can hike and boat.