If you are powering the fronts with an amp, you have to cut the wires behind the headunit or disconnect them at the speaker. The speakers can only be powered by one or the other, not by both. You could come into play where you would heat the wires so much you will melt the insultaion of cause of the power running through them. What are you RCA'* from the amp plugged into if you have a stock headunit. Is it the lil box wires coming out of one side are RCA outputs on the other side?

you used it correct

Road rash - Like I said before, I am not using RCA'* - the amp has line level inputs.
By tying in inside the door, I did mean disconnecting, since I put new speakers in.

Ok sorry misunderstood you. Did you get a chance to get your amp bench tested to see if its working fine. Or get a hold of the amp manufacture'* technical support. That could be your best bet.

Well I have determined it is the sub causing the problem. Amp works fine powering four speakers. As soon as I try running two speakers and the sub it kicks it into protection. I even bypassed the sub box terminal and used new wire directly to the sub. So now I am in the market for a new sub. Here are my amp specs -- any suggestions?

The amp is a JBL 80.4 --

Power Output 4 ohms 40wx4
Power Output 2 ohms 80wx4
Power Output 4 ohms bridged 160wx2
minimum impedance - 2 ohms
frequency response 10hz-50khz
input sensitivity (rca type) 250mV-4V
THD + Noise (4 ohm) 0.05%
signal-to-noise >100dB
maximum current draw 43 amps
fuse requirement 20Ax2