In the 6th gen accords... the factory headunit does not have a "remote turn on" output... meaning since you have amps hooked up to it, the shop that put them in probably wired the amps to come on whenever the key is on... so weather your deck is on or off, the amps are still on. Being that there is no signal going to the speakers in the car, they act as a microphone for the amp... (a real microphone is essentially a small speaker, when vibrations cause it to move, it produces an electrical current) and you know what happens when you put a microphone in front of a speaker... you get FEEDBACK!!

You may want to try putting a switch on the remote turn on for the amp... that way, when you turn the deck off, you can switch the amp off too, so you wont get feedback.

Another way around this, is to get a new headunit. (I have a pioneer fhp-4400 for $100 )

Adding subs to a factory headunit is not a bad idea... they arent nessecarily the best sounding decks in the world, but they do work.