best places to stay

In Prague we stayed at the Hotel Hastel, just a short walk to town square (Rick's group was staying there at the same time, was tempted to say hello, but didn't want to impose)
In Cesky Krumlov it was Castle View Apartments, right in the center
Both places served a nice breakfast. Hotel Hastel had tea/coffee service in the lobby and wine In the evening. Castle view was an apt so we had all amenities.
Both were in Rick's book.
In Budapest we stayed on the Buda side at the Hilton. My hubby gets a nice discount so we didn't really have a choice. If choosing, I would stay on the Pest side.

We look for B&B's with character and charm, great breakfasts, and perfect locations.

Prague - the Green Garland Pension. We loved this location because it was right across the bridge and we could make a stop in the middle of the day during our wandering of the city. They had hot tea available all day and we loved the ability to stop, enjoy a cup, and regroup for the afternoon exploration.

Budapest - the Brody House. This eclectic hotel is in one of the few remaining palaces of the city. It was perfectly located to visit the many Ruin Bars - you must go visit Szimpla and Mika Tivador.