A control system is provided for automatically setting up and controlling a climate control system for a building having one or more zones and one or more thermostats in communication with the associated heating or cooling components of the climate control system. In some embodiments, the climate control system comprises one or more heating or cooling systems which may be controlled by one or more thermostats. In other embodiments, the climate control system comprises a thermostat, a heating and cooling system, one or more remote temperature sensors corresponding to at least some of the one or more zones within the building, and one or more dampers corresponding to at least some of the one or more zones within the building.