I'm just thinking if audyssey EQ'd them and set them to large then we know that it won't offset Audyssey's special EQ effects. I think it just sends the same bass frequencies to both the towers and the sub correct? If this is so does it take away from the dedicated sub? Like less bass if it is going to both towers and sub?
Batpig has given you a superb answer - you may also care to look at the FAQ, here: