A thermostat and related methods is provided for controlling an HVAC system having one or two separate transformers for supplying power to the HVAC system. The thermostat includes isolation circuitry housed within the thermostat to safely connect to the HVAC control wires and power wire(s) whether the HVAC system has one or two separate transformers without the use of removable jumpers or manual rewiring. The thermostat can include a processor that sends DC signals for turning on and turning off each of the HVAC functions, and an isolator adapted to electrically isolate the processor from the control wires and power wire(s). The isolator can include a transformer, such as a low cost Ethernet transformer. The circuitry can include one or more field effect transistors adapted and arranged so as to open or close an electrical connections between the control and power wires, thereby turning on or off the associated HVAC function. According to some embodiments, the Rc and Rh terminals are permanently connected using a fuse.