The stock Wrangler subwoofer is a 1 ohm sub, and the normal replacement sub that you'll buy at best buy will be a 4 ohm speaker. You can buy nicer subs that are 2 ohm, but it still won't be stable at 1 ohm.
What I'm getting at is that a replacement speaker paired with the stock amp won't sound good. It may sound better than a totally blown speaker, but probably not much.
A better idea would be to get a small amplifier and mount it under the driver's seat, then wire it to a nice replacement sub (well, as nice a sub as you can get in a 6.5 size). One problem with this setup is that the stock head unit doesn't have any rca outputs, so you'll need an amp with line inputs, or some line to rca converters.
I started out doing something like this, and ended up with a new head unit, and subs mounted inside the rear seat.. things mushroomed quick..