Mary's is a friendly Czech-run accomodation agency with an office in the streets behind the museum in Wenceslas Square. Their service is quick and efficient (I have always found that they reply within the hour if you email during office hours) and, although they offer the usual hotel booking service, I particularly recommend the apartments which they own and manage. Check out the location of their apartments on Husova - excellent value, right in the middle of the old town, and a place where you can come and go as you please.
Is this your business?