If I understand what you're saying, you're talking about the mechanical connection from the actuator to the door lever. Just determine what direction it operates and what the position should be by comparing the two from side to side. With it plugged in, but still not connected, mechanically, you can operate it using your HVAC control and put the rotor portion in the correct position.
No worries - just take a break for a bit and look at what is happening with the door, then at what happens with the actuator when operated and bolted in position. You'll get it.