Prague is an amazing city, full of history and picturesque settings. However, it is an old city and even with advancement in disabled access, it can be difficult to get around....but not impossible.
A few hints can help you enjoy your time here in my adopted city.
1) The Prague tourism office provides a free handicapped guide to the city that includes parking spaces, areas that require companion assistance, etc.
2)Refit your wheelchair with larger front casters or purchase a GOFreeWheel adaption. This makes life here amazing and cobblestones, small curbs, and tram tracks are not a problem.
3)Rest rooms for the disabled are available in certain locations, especially at the big landmarks like Prague Castle. But other locations are difficult to find. Most major malls or shopping centers are fine and if you do need to use a restroom in the tourist areas, they are free to you.