I just, literally this morning, fixed the crap job that best buy did wiring my 2011. It won't get deep into how crappy it was, but the didn't ground it correctly, and they basically just ripped out the dash to get it in, while breaking some of the plastic in doing so)
It sounds like you have the base head unit like i did, so here is the deal....it is just like wiring any auto with a factory head unit ( splice into connections to feed the stereo signal to the amp and then to the speakers, etc...). But, there is zero point in doing this if you don't get a line out converter to correct the output on the factory stereo. The stereo is configured for the shit of excuse for factory speakers, meaning it is greatly reduced so it doesn't blow the paper cones. There are plenty of posts about this.
The Line out converter will correct the sound, and deliver the tones that the aftermarket speakers (not to mention the amp) need. I would highly recommend any product built by Audio Control. I got the LCi-6 and the difference in sound is incredible!!! I mainly listen to metal, rock, and talk radio. All of it sounded fantastic, and I have yet to even put in the after market tweeters and sub. Already so much better than stock. This is the one I bought from Amazon: http://www.amazon.com/AudioControl-L...&keywords=lc6i
. The company makes plenty of versions, so find the one that suits your need.
As far as installing the LOC....also a breeze if you have wired an amp before. Just think of it as a pre amp and install it in line between the stereo and amp.
I know you have speakers already, but I am also going to throw this out there. A jeep is made to ride topless, constantly in the elements. So, you need to make sure you have weather resistant or marine rated speakers. I highly recommend Polk. All of their products are water resistant,and I think sound amazing.
Let me know if I can help. I was where you are several months ago. Good luck!