muffled bass

Hey guys, I'm a newbie to this site and to car audio but I have a question regarding my subwoofer.  I know this is more of a "Car" audio website but my question is in regards to my system that I had installed in my boat.  When I first bought the boat last summer, it came with (4) "door" speakers.  Me and a friend of mine replaced those factory speakers with (4) kicker marine speakers and we also installed a 6 channel (I believe) JL Audio 450 watt marine amp and a JL Audio 12 subwoofer in a sealed enclosure.  The (4) speakers sound great but I've got a concern about my sub.  We placed the sub underneath the sundeck, in the engine compartment.  When the sundeck/engine cover is closed, the bass is muffled and is barely noticeable.  But as soon as you lift open the sundeck/engine cover (even if the cover is open by as little as 4 inches from the closed position), the bass becomes alot louder and is really a night and day difference.  It really sounds good like this, but of course I can't really drive down the lake with the sundeck open all of the time.  What could possibly be my problem?  Do I need a different sub enclosure?  Or do I have another problem that needs to be addressed?  Any feedback would be greatly appreciated!  Thanks!

It's a 2002 Chaparral SSi 216 (21.5' long) bowrider.  As for the sound barrier, first off the sundeck/engine cover is covered in foam for cushioning, and second the bottom side has some type of foam (almost looks like egg crate), so maybe that does have alot to do with it.  But I was just wondering if there was anything I could do to get better sound out of it.  There really is no other place that my sub can go...it's just to big to fit anywhere else.

Here's a picture of the boat.  The sundeck/engine cover is at the rear and has that black stripe running across it...