A system PDA-based on line diagnostics for automatically discovering a thermostat configuration, turning off normal controller delays, temporary overriding sensor inputs and set points, and verifying proper output action including the monitoring the discharge air temperature for the resulting temperature behavior based on the equipment stages activated. The diagnosis may include the testing of sensors, set points, the fan, cooling equipment, heating equipment and the wiring connecting the controls with the fan, and the cooling and heating equipment. Problems discovered may be reported, automatically recorded and the original operating parameters may be restored.