DGUY - Please keep in mind that I'm at a disadvantage here, no instructions and I haven't installed one of these but this is what I think is happening based on your pictures. The power and ground that actually runs everything is being supplied by the large red and black wires that you ran to the Pulse Bar Buss which go to the battery. The small red and black wires (top left hand side in your picture) is what actually triggers the function to happen from the remote switch. If that is the case then I see no reason to use the two pin connector since both pins go to 1 wire I don't even understand why it would be split into 2 pins. (what's the point?) What does that connector plug into? What side of the wiring harness is it on? Assuming the connector is going to the battery only I would wire it as I suggested above. If there are 2 red wires coming out the other side of the plug that go different places than that is a different story.
The black wire to the black Pulse Bar plug. The red (hot wire) to the yellow (accessory only) Pulse Bar plug. If you wire it to the Red Pulse bar plug wire it would be "HOT" all the time which is what I think your trying to avoid.
If anyone here sees this differently please chime in. I do not claim to be an expert but have wired plenty of shit in my day and this seems to make perfect sense to me.