As bobdole stated, I'm almost certain the problem lies with your sub amp. If it isn't the sub amp, then it could possibly be crossovers.
You even stated that when the sub is off, the front speakers sound fine, but when the sub is turned on, you end up with distortion. This is most likely caused by a grounding issue or (though this is quite unlikely) your RCA/speaker wires are too near your power cables. I had this same problem in my PT.
To check to make sure that it's just the amp, disconnect the subwoofer from your amp, but leave the amp connected and ensure that it turns on with your deck. This negates the effect of bass on your hearing. If you still have interference when the sub amp comes on, then it's definitely one of the two issues I just mentioned.
I patched the problem temporarily by adding a ground loop isolator ($15 or so at Radioshack) but eventually I looked into the theory of hypergrounding and ran a couple wires from my battery to 3 places: common ground point in the engine compartment, the ECU and the camshaft position sensor. I was skeptical of its effectiveness, but figured I'd test it out. I removed the ground loop isolator and no longer had any interference whatsoever.
Now, my problem is that I'm pushing 1200+watts RMS total and even the hypergrounding deal is keeping my headlights from dimming and I need to install a cap.
