You should be able to run it right though the amp. The ground wire and the 6 pin harness that connects the radio and CD player together you can take out. Leave the stock power and audio harness plugged into the amp and the output plugged into the amp. directly plug in your new harness. You can also take a battery and attach each pair of speaker leads to the battery terminals and pop the speakers, go down the line (that is on the amp inputs, out puts, on the radio) to check where the signal is lost.