I've got a 2001 and I ran the speaker wires straight to the speakers. The stock wiring is probably 20 or 18 gauge which can impact the sound of the speakers at higher volumes (too much power going thru too small wires).

I ran 16 guage straight to the speakers from the amp mounted on the back of the add-a-trunk.
_________________________
10+40 Gig Mk2a... with Tuner. S/N 040103784 || 2001 Jeep TJ, 60th Anniversary Edition