Ok, so I have done some research on this jbl thing, and I will admit that I had no idea the major differences between the regular Entune system and the jbl system.
The way I see it you have a few options;
1. Leave everything alone.
2. Replace the entire system
3. Check the resistance of the jbl sub. If by some chance it is 2 ohms, buy a dual voice coil 8 to direct swap. If the jbl sub is 4 ohms, verify that the jbl amp is stable to 2 ohms and you can still direct replace.
4. I am not sure if the jbl amp runs the entire system or if the doors are powered from the headunit. If the amp only powers the sub, you can replace the amp, if not you will either need to replace it with a 5 channel amp to run the whole system, or keep it and get a 2 channel amp to drive just the sub. A new amp should have a new power wire run from the battery, and a good ground as close to the amp as possible. You could then pull out the rear plastics behind the rear seat, one side can hold the amps, and the other build a box for a dual voice coil 10 provided you have enough airspace to deal with. The Kicker comp c line is pretty forgiving on airspace.
If you run a separate amp for sub, you will either need to get an amp that accepts high level inputs, or do an inline low level converter. This should use the existing leads going to the jbl subwoofer.
A lot to digest, does this make sense?
One thing to keep in mind is on the airspace. The rear of the cab is designed in such a way that it limits you on the size of your box because of the pressure equalization flaps midway up the back cab wall, and the power rear window motor, so you are limited to a box built to fit from the floor to the midpoint of the rear cab wall.