1stwave,
The progrmming is the easy part. You have not gave enough details to know what brand and model thermostats that you are using, but the following would apply in most cases.
To control two HVAC units from a PLC using only the thermostat circuits requires modifying the wiring of the thermostats. Think about it: The PLC must have an input from each thermostat to tell it when the thermostat is trying to run the HVAC unit. Then The PLC must have two or three outputs (Heat, Cool, Fan) to each thermostat to interrupt the normal thermostat functions and instead allow the PLC to determine when each HVAC unit will actually run. All this must be accomplished without interferring with the normal thermostat functions. If your PLC has 24 VDC inputs and relay outputs, then maybe it will be easier. Otherwise you will need 2 input relays and 2 output relays.
I have attached an Excel spreadsheet file which illustrates the problems you are facing.