Relay harness problem

Started having a flickering problem a little while back so I purchased a relay harness. I used the fuse box connection as my positive and ran the ground to the battery. Car would turn over but not fire. I moved the positive side down to the battery and ran the ground to another location, same result. I put all of the wiring back to stock and the car turns over just fine. Are the electrical systems in these late models that sensitive or am I missing something? Any input is greatly appreciated.
 
I do have the remote start but it is factory. I also have an amp wired up (300 watts) in the car as well and I run that from the positive side of the battery. It seems like the car isn't receiving enough power to keep the spark plugs firing but it turns over just fine. I am going to try and disconnect the amp and wire up the relay harness without it to see if I am pulling too much power with both (not sure why it would since the headlights do not pull that much).
 
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