An HVAC controller may be programmed to execute a guided set up routine that may guide a user through configuring the thermostat to control a particular HVAC system configuration based, at least in part, on which wires from the HVAC system are connected to terminals of the HVAC controller. The guided set-up routine may be accessible through a user interface provided at a remote device that a user may utilize to interact with the HVAC controller from a remote location.