I have the subwoofer, dealer installed, and its great. I too didn't like the fact that the bass it put out was really loud, and really boomy (too much upper-mid frequencies).
BTW, on the back of it are two black plastic, unmarked, inset, phillips head screws. One of these controlls the amplitude (volume) of the sub, and other controlls the cross-over frequency (i.e. how high up in frequency the sub will produce).
Turn both of these down (counter-clockwise) as far as they go. This will have the sub putting out only the lowest frequency base (i.e. "sub-woofer"), at the lowest possible volume. IMHO, this is perfect for most music, and you can of course adjust it further with the bass control on the dash.
This sub then puts out amazing really low bass, and it's really powerful, without being overbearing. Turn up the aplitude if you want it overbearing =P~
It amazes me that DC doesn't know enough to put that in the "manual" (if you could call it that), or even label them on the back.