Systems and methods for the auxiliary stage control of multistage thermostats are disclosed. An illustrative multistage thermostat for a multistaged HVAC system installed within a building or structure can include a processor having a control algorithm adapted to operate the thermostat in either a normal mode for achieving rapid temperature changes within the building or structure or an economy mode for conserving energy usage. In the economy mode of operation, the thermostat can be configured to determine a target time for achieving a temperature setpoint by either delaying or suppressing activation of the system's auxiliary stage. The target time can be adjusted in part based on the past usage characteristics of the auxiliary stage, the behavior of the user, and/or the progress of the primary stage in achieving the setpoint change without operating the auxiliary stage.