I just went though this whole exact thing, replaced my busted motorized antenna with a cheap aftermarket unit. It has been a headache from day one.
Here is the best bet, and the route I'll be taking as soon as the weather warms up enough for me to work on the Jeep again, Crutchfield has replacement Jeep Cherokee antenna for $10. I tried several different ways of connecting the two coax cables together with the aftermarket and never really got good signal, in fact it came so loose after a few miles that I get none at this point, most connectors won't hold with the vibration of being in a car. I' going to feed the cable from the new antenna into the passenger side kick panel and link up the two coax lines there, so that I can mount the lines to the body where they will be protected and not as vibrated.
I might just get a little crazy with the whole thing though, I hate my head unit and the speakers sound OK with the radio, but the Fleetwood Mac CD sounds like crap. I would like an amp too.....and some sound deadedning in the back....