keepin factory subwoofer, 03 expedition

Hi I have an 03 expedition Eddie Bower, I wan to install an aftermarket radio, the vehicle has 3 harnesses, 1. 16pin harness, 2. 8pin harness with 4 wires. and 3. a 21pin harness with 11 wires. I bought a wiring harness for this specific vehicle which came with 3 plugs one for each vehicle plug. I wired the aftermarket harness to the radio and than plug it to its vehicle corresponding plug. everything works, except for the factory subwoofer. so my question is how can i get the factory sub to work with my aftermarket radio???Knowledge is Power.

Use this as well to prevent turn on popping noise http://www.metraonline.com/part/AFDI-5V