Adding Krakow to our trip, where to add

We will be visiting Budapest, Vienna, Dresden and Prague in June 2014, a long way off but we are using points to buy our tickets this May. Starting in Prague is also a possibility. We would like to add Krakow to the trip, there will be 6 in our group. Initial thoughts are to add Krakow as the first or last stop, since it is hard to find direct trains and to minimize travel time. We are leaning toward a night train from Prague to Krakow, and fly home from Krakow. Is there a better way to sequence the cities? Any suggestions to make the trip more enjoyable? Thanks