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@Keigo @YingYing Tai

It looks like in the EnergyPlus source code, this warning is triggered by the following code:

    } // loop over NumStageControlledZones
    if ((inputProcessor->getNumObjectsFound(state, "AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed") == 0) &&
        (inputProcessor->getNumObjectsFound(state, "AirLoopHVAC:UnitarySystem") == 0) &&
        (inputProcessor->getNumObjectsFound(state, "SetpointManager:SingleZone:OneStageCooling") == 0) &&
        (inputProcessor->getNumObjectsFound(state, "SetpointManager:SingleZone:OneStageHeating") == 0)) {
        ShowWarningError(state, format("{} is applicable to only selected HVAC objects which are missing from input.", cCurrentModuleObject));
        ShowContinueError(state, "Model should include one or more of the following objects:  ");
        ShowContinueError(state, "AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed, AirLoopHVAC:UnitarySystem, ");
        ShowContinueError(
            state, "SetpointManager:SingleZone:OneStageCooling, and/or SetpointManager:SingleZone:OneStageHeating. The simulation continues...");
    }

Essentially, if the model is missing all four object types mentioned in the warning, then the ZoneControl:Thermostat:StagedDualSetpoint object type will not work. However, if you have even one of those mentioned object types, then it should work. In other words, a model should correctly apply the staged dual setpoint thermostat to an air system with:

• An AirLoopHVAC:UnitaryHeatPump:AirToAir:MultiSpeed object, regardless of setpoint manager
• An AirLoopHVAC:UnitarySystem object, regardless of setpoint manager
• Any AirLoopHVAC object, as long as SetpointManager:SingleZone:OneStageCooling or SetpointManager:SingleZone:OneStageHeating objects are used