i just went through all of this......
Its a huge pain if you have the RER radio (2008+). I guess the non-touch head units will work normal. I have also read that its a possibility that the non-nav RER might work fine. But if you have the RER with the nav, be prepared to get frustrated.
You can't really hook it into the head unit of the RER. You would need to spend a lot of money on a PAC unit that converts the signal from the canbus to an analog audio signal. I believe they are around $150-200 and even those are reported to have issues, and possibly not work at all.
I tried everything in my power to splice in my line out converter behind the head unit. I found the wiring diagram and cut and spliced the converter where it normally would go, but it won't work. Let this be a warning, don't waste your time messing with your head unit unless you have the PAC harness.
You could test your luck with the PAC, or get a new head unit, or.......
Its not the most ideal way, but you have to splice the line out converter into the analog OUTPUTS of the stock amp. So basically your new amp is getting the signal from your old amp. Its not going to achieve the best sound quality, but I can tell you that it is still MUCH MUCH better than the stock system. I also have a sound ordnance amp /speakers / 2nd amp/bass. And I installed all new 4 door speakers, and ran new speaker wire.
Take a look at my thread here for more detailed information:
In the simplest way that I can put it, the jeep sends all of its audio information digitally to the stock amp via the CAN BUS. Its a digital signal, so you can't splice into it (you need analog). Also its supposedly encrypted. What those PAC adapters are suppose to do is take the digital signal from the CAN BUS, and convert it to an analog signal, that you can then use to add a new amp. So all of the audio signal to the stock amp is via CAN BUS. But the output signal from the stock amp is true analog signal to the speakers. So you can do what I did and splice into the outputs of the stock amp with your LOC. But keep in mind you will be using BOTH amps this way. It would certainly produce better sound quality if you could splice directly into the head unit with the PAC adapter. But I have read from a few places that it works, and a few places that it doesn't.