[Johnny on another level !]

Hey guys and gals, I just purchased this PWM controller from Brand X. It has directions for wiring it up to a factory vehicle. My problem/question is how would I wire it up having dual alternators? They have 3 pins so I bought a harness and spliced it into the factory harness for the second alt.I only have 2 of the 3 wires going to the 2nd alternator.
Thank you in advance for any assistance!!!