I live in a 4 story townhouse - furnace in the basement. I have two thermostats with ON/OFF switches. In the winter, I turn the main floor tstat off and turn the basement tstat on. The house heats the basement to the tstat setting, and, by adjusting the vents, I can keep the upper 3 floors comfortable as well. In the summer I turned the main floor Tstat off and the basement tstat on for the AC. However, when I turn the fan from auto to on, it runs the compressor continually and doesn't let the temperature setting in the tstat turn the system on and off. Any suggestions?

Call a professional HVAC contractor and have them check into installing a zone damper control system on your system. This should solve the problem and allow you to operate two separate thermostats correctly. This is a complex issue and requires much skill so trying to describe all here would not work. You might search Google under HVAC forced air zone.