Anybody know anything about subwoofers?

Just realized that the preamp signal from the ipod could be different from the deck. It's possible the gain setting on the amp may need to be adjusted to accommodate the deck's signal. Don't want to go too high, though, because you don't want to introduce clipping into the signal. Some info that might help:

1. What device are you using to connect the ipod to the amp directly?
2. What are the current gain settings on the amp?
3. Amp model/specs.