Terry,
I dont know how the Sub is mounted in the stock Jeep, but I do know a thing or two about installing car systems (I work for Sony / Audio MArketing), so any help you need, feel free to ask...
Now, my first advice would be that you should replace your ENTIRE sound system with a Sony system... LOL!
Just kidding! Anyway, most subs will not require RCA plugs, although they are prefered. You can also use the speaker lines as inputs to the amp (subs of 8" and more are ussually powered by separate amps), and use the amp's crossover to regulate the frequencies. Of course, you will loose some sound quality, as the imput is not ideal, but it should work fine, and given the amount of road noise in a Jeep, you should not notice much difference (if any).
I have a YJ personally with (you guessed it!) a Sony system, so I am not sure on the stock setup at all. It is possible that the sub is used as a passive unit, meaning that it is basically a speaker that is limited only to low frequencies (typically 120Hz and under, although sometimes all the way down to 70Hz).
What I did in my rig is that both the amp and the sub are mounted in a way that I can take the entire thing down (mount for the amp complete with amp and HD radio tuner and sub) by unscrweing 2 screws and disconnecting 9 wires (this takes me about 10 minutes). Since I have a hard top, the system is typically in place, but when the top is off and I want to cruise around, I will take out the sub. If I go offroading, I will take out all the amp and HD tuner assembly. Plus, the face of my system is detachable, so that leaves the Jeep with me...
Here are some pics of my set-up to give you an idea of how everything is installed (I think I've posted these before, but anyway):
Main unit and kick panels under doors:
Sub unit and main unit:
Rear speakers:
The amp/HD tunner setup is under the driver's side. I basically made a stand with playwood, covered it in black sumbrella (water proof fabric), and installed the amp on top (so head can escape easily) and HD tuner on the bottom so that both units are higher than the floor of the Jeep (in case I spill something or do something stupid like not taking the setup out and going through a river!).
Both the HD tunner and the are fed through an independent fuse that I can take out and disconnect electrical flow (so I can leave the cables in place when disconnected)
I hope this is helpful!
Felipe