The noise is there because the amp is not properly connected, a quick solution is to reduce the gain for the front channel, most of the installers treat gain as volume control, resultantly it kills the surround and quality. Gain is there to adjust distortion, its not a volume controller.
The correct way of connecting amp is getting the RC Cable from Tracking World/Honda, it has a proper Remote wire connector for the amp so that amp only turns on only when the system is giving audio out put, else it remains off. Most probably the installer has used a high to low converter local box for getting RC leads.
To tune your setup just set the equilizer to flat, take volume on you android to 75%, diconnect the woofer input, take gain to zero for front speaker, gradually increase the gain to a point where your front speakers are about 10% louder than the rear. adjust hpf accordingly to curtail distortion
Now reconnect the woofer input, play a high bass track, adjust the bass boost to mid if you like more bass, I personally prefer to keep it off, now move the gain to max and gradually adjust the lpf to a point where you don't hear any distortion, now gradually reduce the gain to a point where you feel the bass is adequate. Remember gain is not volume controller, its an adustment to minimize distortion.
