Nope, won't affect your sub if you wire it up properly... I believe you need to tie the wiring for your headunit into the power antenna wire for the sub or something like that. I can't remember how the wiring is now...the blue wire from the jeep powers the sub I believe. That should go to the power antenna (blue & white) wire from the headunit. I may have that backward...if it doesn't work one way, try it the other until the sub works. lol
Anyway...that's the only wire you need to worry about, just the wire that kicks the amp on. The signal comes from a line out converter in your Jeeps speaker wiring and you won't be messing with that.