I have two themostats one upstair and down stairs. I want each to control its floor.

And..

Well I'm not surprised you do. But unless the system was designed to have two zones... and you don't have an easy path (EG on open stairwell) between floors then what is your problem? Did you just stick a second thermostat on a one zone system?

You have to give more details than you have.

Is there a zone controller on your air handler?