Remove rear passenger side paneling. Unbundle the wiring mess at the amp. Check out wiring diagram posted above for the sub speaker wires or just cut the wires near the sub. These will be your speaker level inputs for the sub amp. Make sure your sub amp has speaker level inputs or you may need to buy a line output converter (loc). I first used a cheapo Pac loc but the line level output was really weak. You may have to do a little trial and error with the amp gain or get a powered loc (Audio Control) and see if you can get enough volume.
I think there should be enough space behind the panel to fit a small sub amp. Get an amp with a remote volume control or you can put a line level volume control between the loc and the amp but this is less desirable (I think).
And do change the sub. All of the above is a total waste if you don't. You will be shocked at the "flimsinest" of the stock JBL.