OK so you want to use the factory JBL headunit with the indash 6 disc changer, right?
Basically you will find the speaker wires that are coming out of the amp and label each wire to which speaker it is going to. Then take those speaker wires and wire them to the LOC, the LOC will have 4 set's of wires.
Heres the colors of the factory amps speaker wires.
The front left pos. is pink
The front left neg. is purple
The front right pos. is light green
The front right neg. is light blue
The rear left pos. is black
The rear left neg. is yellow
The rear right pos. is red
The rear right neg. is white
The ACC turn on lead is a small light grey wire, you can tap into that for the turn on lead for the new amp.
From the LOC you plug in your RCA cables and run them to the new amp you are going to use. Make sure to run the RCA cables on the opposite side of the car as your power wire for your amp.
Make sure your 4 channel amp is bridgeable. Then make sure whatever speakers you are putting in can handle the amount of power the amp is going to be sending them. You can overpower the speakers a certain amount, you will just have to have the gain turned down a little.
Check out the JL audio tutorials for more info.
http://www.jlaudio.com/tutorials/index.html