morgan,
Personally I like how Wetsounds has configured their EQ because I consider the subwoofer as an integral part of the in-boat zone. The bass control is actually the amplitude adjustment on a paragraghic EQ. But I understand how your need is different.
The simple solution would normally be to add a sub level control if your subwoofer amplifier has a provision for this rather than just a bass boost control. However, your intended usage requires a different route. In your case, use a PAC LC-1 in line after the EQ in-boat output. This way you can raise the level of the in-boat zone on the EQ and attenuate all the in-boat coaxials with the PAC control.

David
Earmark Marine