Without knowing how your controller is configured and what are the systems being controlled, it is a bit difficult to provide specific answers. In the appropriate configurations, the cooling system is controlled by the Y wire. I suggest you look at the wiring diagram for different configuration available at this site.
http://www.emersonclimate.com/Documents/White-Rodgers/Catalog_2010/2010_Cat_pg_157.pdf

A full instruction manual is available at this site and provides different operational modes which may not require that you take out wires but you can isolate the control using the selector switches inside.
http://www.emersonclimate.com/documents/white-rodgers/instruction_sheets/0037-6585.pdf

When working with the unit be mindful that full mains voltage is connected directly to it.