I just got a aftermarket radio to work with the factory Fosgate amp.
Here is a quick write up of how to do it:
This write up cover the non-nav system but it will work with both. Please read the hole thing before attempting this. And of course I take no responsibility for any problems you may have.
The stock amp uses the Can-Bus system to turn on the amp, control the amp, because of this I thought I could disassemble the factory head unit and use parts of it to keep the amp working but then splice in the new head unit speaker wires. Thats just what I did.
Unplug the front part of the radio from the dash. Its the small plug on the 4-way/airbag light button piece on the bottom of the radio face. Do not disassemble this yet.
Take out the four screws holding the radio box in the dash and unplug the two cables from the unit.

On the bigger connector (of the two) splice (DO NOT CUT) into the Red W/white wire and solder it to the constant 12 volt wire on the new radio harness.
Splice the black wire to the ground of the new radio harness.
Splice the yellow wire to the switch 12 volt wire (ignition) of new radio harness.
CUT the white wire to the front left + speaker wire and solder it to front left + the new radio harness.
CUT the black wire to the front left - speaker wire and solder it to front left - the new radio harness.
CUT the red wire to the front right + speaker wire and solder it to front right + the new radio harness.
CUT the green wire to the front right - speaker wire and solder it to front right + the new radio harness.
NOTE: the factory amp only gets the front left and right speaker wires going to it. The amp splits it up to front, rear, and sub.
I took apart the factory radio and removed/unplugged the six-disk changer in the top portion of the box. It was dead weight and not needed.

I carefully placed the factory radio into the hole deep in the dash behind the HVAC controls making sure the plugs were facing up. Make sure its snug and wont move around. Plug in both connectors to the factory radio. Now plug in the new radio connector. this is just to test and set up, you don’t need to mount it yet.

Turn the new radio on (ACC on ignition) so a CD or something is playing. If you have had the factory radio unplugged for more than 5 minuets you won’t hear any music. This is normal. Now plug the small connector (4-way/airbag light button piece on the bottom of the factory radio face) to the harness in the dash. Make sure the hole factory radio face is still connected to the 4-way/airbag light button piece. Push the power button on the factory radio face and turn the volume up. You should now hear you music.
First you need to set all settings in the factory head unit to the desired settings. I set the balance, treble, bass, etc to default because I want the new head unit to control that. You must set the volume to the max setting you want the new radio to have. Think of it this way, The main factory system volume will control the gain on the amp the new radio controls the volume between 0 and what ever you left the volume at of the factory radio.
Once that is set up unplug the factory radio face. You will find you need to unscrew and remove the 4-way/airbag light button piece on the bottom of the factory radio face and mount it on the new dash kit. Clean up your wires neatly and mount the radio in the dash. Plug in the 4-way/airbag light button piece and snap on the dash kit and your done.


Now here is the down side. If you disconnect the battery from the car the Fosgate amp will default to OFF. You would need to reconnect the little ribbon cable between the 4-way/airbag light button piece and the factory radio face you removed it from. Then press the power button to turn it on. Because of this I will remove the PC board from the radio face and mount it in a box behind the dash with a remote mounted button soldered into the power button spot on the PC board. That way if the battery gets disconnected I can reset it with a push of a hidden button.
Please post any questions you have, thanks and good luck.
Brian-
Finaly they came out with a real solution!
Thanks Boy36, he started a thead about the new Metra MITO-02. This allows you to use the stock amp with out my mod.
Heres the link:
Metra MITO-02