I stayed at the K+K Central in Prague and the K+K Palace in Vienna, and was very pleased with both (I have a booking for the K+K Opera in Budapest for Feb. 2007) I booked off the hotel site online, but make sure you check for specials, which are as much as 100 euro less that the posted rate. (I think I paid about 120 euro for a double room at the Central).
The Central is in a better location than the K+K Fenix in Prague, very near Old Town Square and the Municipal House and within walking distance of a metro stop. On a quite side street and very clean and confortable rooms, excellent breakfast buffet and helpful staff. In Prague a trip to Karlstein castle is a worthwhile daytrip. In Vienna the K+K Palace is slightly off the beaten track, but still near public transport (and just around the corner from an airport bus stop) and is quiet - about a 10-15 min. walk to the Hofburg.
In Prague don't miss the Strohov monestary (http://www.strahovskyklaster.cz/)- splendind baroque library and excellent beer hall, featuring beer brewed by the monks. It is near Prague Castle. The opera is quite cheap in Prague and you should try and attend a "black" theater performace, very unusual mutli-media presentations.
I think 3-4 days would be sufficent for Prague.