A thermostat includes a processing system configured to control an HVAC system. The thermostat may also include a plurality of HVAC connectors configured to receive corresponding HVAC control wires, and a connection sensing module configured to determine the identities of HVAC connectors into which corresponding wires have been inserted. The processing system may be further configured to identify, based on the subset of HVAC connectors, whether (i) only a single possible HVAC system configuration is indicated thereby, or (ii) multiple possible HVAC system configurations are indicated thereby, resolve a particular one of the multiple possible HVAC system configurations that is applicable, and operate the HVAC system according to the HVAC system configuration.