well, when it plays deep bass, the cone will move alot more than other notes, typically, and, depending on the tuning of the box, the sub, and wear, it can go beyond it's limits and the coil former(basically the sleeve that attatches the cone and coil, and moves around on the magnet) can hit bottom (the back of the magnet) many amps have some sort of sub-sonic filter. what this does, is turns down the deeper bass at certain settings/frequencies, so that it doesn't push the sub too far. feeding distortion is basically what happens when you turn the bass up on the deck, and crank it. your mids/highs will start to distort and sound like poo......well, even with the amp turned down, you are sending the same crappy signal to the sub amp and it will play what is called a "cllipped signal" aside from it not sounding good, what it does is basically keeps the sub powered longer than the rest/return periods in the sound wave. simply, the sub moves less, but generates more heat.
so basically, if your deck sounds like crap, adjust the settings, and don't let the sub bottom out.