[...] To mimic this I bypassed the potentiometer and tried to send my own signal between 0 and 5 volts hoping that any value I send to the signal pin between these two values would result in a corrosponding power signal to be sent to the helicopter's motor. However the helicopter always spins at the same speed regardless of the voltage I put through the signal pin on the controller.
I guess that you generated the signal by PWM and forgot to integrate it coming from the controller, so, instead of a varying DC level, you just send the raw PWM pulse train (which, with just a little circuit capacitance will be peaked to close to 5V, no matter the duty cycle)?
You could test it by an external variable supply (be careful not to go over 5V!) and wires of the same length that you used with the controller. I guess it will work, but if not, the wires either picks up noise (making the receiver ignore those pulses), or have too much inductance (twist the wires, or at least let them run close in parallel).
For autonomous flight and with the controller interfacing the transmitter, you'd need another transmitter (in the chopper), to return sensor data to close the loop, but it would be better placing the controller on-board, saving you the extra transmitter and receiver.