To deploy reference position changes on to the drone you will have to make the reference value changes inside the flightControlSystem(FCS) block.
To do the same, you can navigate to the following subsystem in the asbQuadcopter model:
flightControlSystem/Flight Control System/flightController/Flight Controller
The reference values are held in ReferenceValueServerBus.
If you overwrite the existing values of X, Y, Z (maybe using a constant block), the reference value will accordingly be adjusted when you deploy on to the drone.
I hope that helps!