First off, if you're going to go through the effort of replacing the factory subwoofer, don't use the factory amp. It's absolute garbage, and even with an aftermarket sub like a Kicker, the factory amp simply can't power an aftermarket sub to sound anywhere near as good as it should.
I recently upgraded the audio (including the factory subwoofer and amp) in my 2005 Rubicon, and this is what I used:
https://www.amazon.com/dp/B00UG7AWH8/?tag=wranglerorg-20
https://www.amazon.com/gp/product/B01BLVEZG6/?tag=wranglerorg-20
That amp is TINY, and it's waterproof as well. It has more than enough power to power that subwoofer, which also happens to fit in the factory subwoofer enclosure with very minimal modifications (you just have to Dremel some of the inner pieces of the factory enclosure in order for the new subwoofer to fit, since it's a little deeper than the stock one).
Anyways, it was super easy to install, and I can't tell you how huge of an improvement it is over stock. Seriously, words can't even describe it. The end result is a subwoofer that totally transforms the audio in the vehicle. I don't listen to bass heavy music (i.e. rap), mostly just blues, jazz, rock, and some twangy country. However, this thing just totally brings the music to life, even with the subwoofer only on half volume (any more than that and it was really starting to rattle things).
You honestly can't even compare the factory subwoofer (or that crappy Quadratec one) to this setup. This is mainly to do with the fact that the factory amp (and the wiring used) is just a complete piece of crap.
It doesn't matter what subwoofer you put in there to replace the stock one, no subwoofer you use is going to sound that great, and it's entirely because of the factory amp. It simply will not power a decent aftermarket sub (or even the stock sub) the way you or I want it to.