The factory amp is setup for a dual voice coil sub. The 4 wires coming out of it are red, black, brown, and white. Obviously red is positive and black is negative, but which is which for the brown and white wires?
There is a ton of information out there about this, but to save you time, you can either use the black/red combo or the grey/brown combo. Test it in your jeep before you finish the wiring and see what works best, the cut and cap the combo that does not work.
I read that there are some differences between 97-02 and 03-06, on mine all 4 connectors were the same size. Anyway, I found my multimeter and tested the leads. On an 05 the red and brown are positive, and the black and white are negative.