I installed an aftermarket headunit (Camecho Double Din Car Stereo 7'') in my 06 with the metra wiring harness and used the double din dash kit. Everything works great except the 8" amps in the doors on both sides. They were working before with the shaker 500 installed and since both aren't working I'm sure I wired something up wrong. I plugged the two rca cables from the wiring harness into the back of the new radio and it doesn't make any noise.

I didn't use the two blue amplifier + and - wires because I'm not sure where they go and I think that might be the issue.

Metra wiring harness I used:
Metra Wiring Harness adapter
shaker 500 wiring diagram:
Shaker 500.pdf

 

It is very tricky with the wiring on that setup. Much easier changing Amps as well as the Unit. I have my Front Door Subs running off of their own Amp.

 

I think you're right, you need to hook up the amp remote turn on wire (usually blue coming off the aftermarket stereo) to the wiring harness for the subwoofer amps. You'll want to solder in a 5V voltage regulator in-line because the aftermarket deck will supply 12V but the original shaker only did 5V. Otherwise you'll get a pop from your subwoofer amps every time the radio turns on

 

Here's a thread I found on the regulator:

https://themustangsource.com/forums/...r-subs-400761/

https://themustangsource.com/forums/...needed-453315/

https://themustangsource.com/forums/...w-pics-471202/