I have a fair amount of experience with audio except when it comes to running aftermarket systems to stock navi HU's. How do I go about this?

 

It can be done, very easily. Do you already have the factory sub harness? If you do, just splice in at the sub end under the back seat. There are six wires in the sub harness, you only need to use 5 of them. The violet-/-light blue is 12v fused amp power (25 amp), the black-/-orange is ground, the dark green-/-violet is amp turn on signal at 5vdc, the brown-/-orange is audio signal + (rca center pin) and the red-/-black is the audio signal - (rca ground or outer ring). Just use the 5v amp turn on to trigger a relay and the 12v as the amp turn on signal to the new amp thru the relay, run your own power to the new amp, and use the audio signal leads and splice them into an rca plug.

 

Can someone elaborate this for me. It sounds to me like i'm running two cables into the amp relay??

 

Bump

 

Check out the PAC adapters. I could be wrong, but I think they make a cable that can plug into the factory cable to add an aftermarket AMP. Google PAC OEMFRD and it will get you pointed to the right website at least.
Hope this helps.