First of all, which factory system do you have? Concert or B&O?
Assuming Concert, the head unit sends a low level signal to the back right corner of the trunk where the amp is located. The amp takes this low level signal from the HU and sends out a speaker level signal to the doors and center channel in the dash.
The low level/input wires are thinner (pins 23-32) and the high level/output wires are thicker (pins 3-20).
Here is a diagram:
You should unplug the factory subwoofer at the subwoofer and just leave that plug hanging. This will turn off the factory sub. Just reach up, pinch the connector, and unplug it.
For a remote wire, look at the fuses in the passenger side of the trunk. You can tap into one for remote, I forget which one. Just look at the list of fuses and use your head.
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