It's been awhile since I've looked in the stock amp area but if I recall correctly the wires down there are of a different color than the pigtail to the speaker in the door. I wish someone would chime in who has also done this and let us know what wires go to where at the amp. The wire schematic I have for the Shaker system shows the wires being the same color all the way to the amp, but I'm 99% positive they're not. I'm not even sure which side of the amp is the output; i.e. the top or bottom connector. Due to that fact I didn't run a remote wire, which was cool because all my equipment is auto-turn on.