Best Places to Stay in Cesky Krumlov and Prague

When? I ask because wondering if AC is a requirement.
Have a wonderful trip!

Pat,
In the end of September-October.

For Prague, look at Hotel Hastal - relatively close to the main square yet outside the touristic crush.

In Prague, I would stay somewhere between the Old Town Square and the Charles Bridge. I stayed at High Heaven and would stay there again.

In Cesky Krumlov, I stayed right by the main square and would stay in that area again.

I dont know your price range, but we stayed at the Hotel Růže in Cesky Krumlov and it was very nice.

In Cesky Krumlov, we really enjoyed our stay at Hotel Zlaty Andel, located right in the square. Such a convenient location for everything.
https://www.hotelzlatyandel.cz/

In Prague we stayed at Pension Dietzenhofer twice. It's located in Mala Strana in a quiet area. It's about a 5-minute walk from Charles Bridge.
https://www.dientzenhofer.cz/

Check out ( or Czech out )The House at the Big Boot in Prague. Excellent location in Mala Strana, walk or tram to Charles Bridge. Opposite the German Embassy in a lovely small square. The owners were fantastic…friendly and helpful. Breakfast was cooked to order and very good. Our room was huge and comfortable. It isn’t fancy but it was a wonderful visit. A favorite of many years of travel. Just plain old nice folks. We were there a while ago but a quick look at current reviews has it highly rated still. We walked everywhere from here. Great memories, beautiful city.

Just did this 2 weeks ago. Stayed in an aparthotel in Prague that I booked via Expedia, it was beautiful, spacious and very inexpensive. The downside was no staff and had an issue with the front door code, also no ability to store bags before or after. In Cesky Krumlov, stayed at Villa Krumlov which was very good and near the center of the town, also very reasonable. In Vienna I stayed in a hotel by the main train station for two nights SMARTHotel Wien which was fine. For some reason I booked another hotel in Vienna for the next 3 nights, the Johan Strauss Hotel. Both were very good and inexpensive, both are very convenient to the U-Bahn Metro so you can be in the absolute center of Vienna in 5 minutes. Everything I booked through Expedia based on good guest reviews, photos of rooms, location and price.

Took an afternoon RegioJet bus from Prague to Cesky Krumlov and then the next day took an evening Flixbus from Cesky Krumlov to Linz, Austria then caught a train right into Vienna, partly why I wanted a hotel next to the Vienna station.

Just did a 16 day trip to Krakow, Prague, Cesky Krumlov, Vienna and Budapest. Didn't spend more that $80 USD a night on accommodations and some of the places I stayed (more on the $70-80/night were almost palatial). Walked so much (~10 miles a day) while not sitting or being inactive that I returned home 15 lbs lighter despite eating tons of schnitzel, goulash, sausage, German pancakes, and beer and wine with every meal.

In Cesky Krumlov I highly recommend the Castleview Apartments - especially if the Attic Castleview room is available. It's close to the square, and even Rick Steve's himself stayed here! (Watch his Czech Republic Beyond Prague video and you'll see it!) We enjoy Airbnb's and have stayed both sides of the Charles Bridge close to the Old Town which is preferable to the area near Wenceslaus Square. We used the CK Shuttle for the first time and found it convenient and the drive between Cesky Krumlov and Prague very enjoyable!

We also stayed in and enjoyed the attic apartment at CastleView, but do check about AC and an attic lodging. I doremember a portable, mobile unit, in the Attic, which usually aren't too effective, but since we were there in early April, didn't need to worry about AC.
We also used CK Shuttle, and highly recommend them.
Have a great trip!