Being that I didn't use any portion of the factory system, I can't really help you there. Someone on the board should be able to help. I just went out and looked at the factory amp directly behind the glove box and I'm only seeing two connections at the amp. One on the left and another on the right. I would assume one of the connections will be needed to by pass the amp. The instructions you received with the wiring harness should have explained this to you. Hold out, someone will be able to help.
Take care.
