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Perhaps the easiest way to force a system to over- or under-deliver heating/cooling via EMS is if the HVAC system (staged RTU in your example) were modeled as a Unitary System. This exposes Unitary System actuators for "Sensible Load Request" and "Moisture Load Request" that you can override with a +/- correction factor to the actual zone loads that EnergyPlus calculates. The Unitary System should then inform all of its internal coil and fan components how to meet the actuator value that you provide via EMS.

If using a Unitary System isn't an option, you could leverage other actuators to override temperature & humidity setpoints at specific nodes and/or fan flow rate.

You might find this discussion about proportional control logic in EnergyPlus helpful, since it's related to this question.