Salzburg should get the 2 days - more to see and do - and lots of good stuff in the countryside.

Cesky Krumlov is good for a day. I was there for about a day and a half but also saw the nearby monastery. It was plenty of time.

I agree with the above. Two nights Salzburg, one night CK. We did a great evening walking tour of Cesky Krumlov through Otto Stromak on the official CK website(http://www.ckrumlov.info/docs/en/atr138.xml)

We also did a fun Sound of Music Bike tour in Salzburg through Fraulein Maria's Bicycle Tours(http://www.mariasbicycletours.com/)

Here is a link to my trip report from Salzburg and CK, along with pictures:
Cesky Krumlov - http://www.fromhometoroam.com/2012/06/cesky-krumlov/

Salzburg - http://www.fromhometoroam.com/2012/06/salzburg-2/

Thank you so much, everyone! It's reassuring to know that I've made the right decision!

Salzburg and Cesky Krumlov are 2 completely different cities. Cesky Kromlov can be done in one day but is so quaint and beautiful you will never want to leave (My husband proposed to me here!) Salzburg is a bigger city a bit touristy but also gorgeous and more cosmopolitan filled with plenty of good food and shopping and lots of culture like the house Mozart was born in. The day trips to lake districts are well worth it ie. St Wolf???

I would do one night in Cesky Krumlov the night is very magical because in the evening you have the whole town to yourself but when you turn the corner you may encounter a random reenactment of a medieval sword off don't forget to check out the awesome underground cave bars

In Salzburg check out the Mozart Dinner at the oldest restaurant in Eastern St Peters (???) beautiful!!!

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I agree, with your limited time, 1 night in CK and 2 nights in Salzburg.

But... if you had more time.....?

i would try for 2 in each... we only had 1 overnight in CK and i'd wish for 2

I hope you can get the time for 2 days each place. Of course travel takes some of your precious time.

I have been to Salzburg more than once and found plenty to do there. We went to Cesky Krumlov on a one day bus tour from Prague. Given that you might have just one 24 hour period in CK, I suggest going with tour. That way you have organization and pre-planned entry times. I am not usually a fan of guided tours - had rather do it myself - but when time is short, a tour has the advantage of preplanning by someone else.

If you are traveling by train, bear in mind that rail connections between the two cities is less than ideal.
Some of the connections require 4 changes.

I am reminded of the tired joke the punch line of which is "Buddy, I don't think you can get there from here."
If your urge to go to both is overwhelming, I suggest you drive.

Why not spend 3 days in Salzburg rather than a day and a half in Salburg, half a day in Cesky, and the rest riding or sitting in a station waiting for the next train or bus?