Re: subwoofer does not sound good
You have two issues here:
First, you need a much more powerful amp to drive a subwoofer.. something that's pushing at least a few hundred watts RMS. Amps are dirt cheap these days and for less than $100 you could get something that would work.. and for $150-$200 you could get something that would melt your ear drums. My HiFonics 1700w class D amp was $200 and I'm driving 2 x 3500w Pioneer competition subs with it @ 1ohm.. and my teeth rattle together if I turn it up. Literally. It's way, way more than I need.
It looks like you have this amp here:
http://www.onlinecarstereo.com/CarAudio/p_18634_Total_Mobile_Audio_T3204.aspx - which is only rated for 60w x 4.. AND this is an off brand.. meaning.. I bet you're putting out like 30w per channel.. you're not driving a sub with that.
Second and actually foremost.. when you're trying to add bass on a boat, it becomes extremely difficult due to the acoustics in open air. Bass frequencies are literally very long waves of sound and they like to resonate in things. When you have subwoofers in the back of your car, the bass waves are bouncing all over the inside of your vehicle and actually amplifying the sound. When you put that same speaker in the open air (ie - on a boat), the waves have nothing to bounce off of and literally just get sucked up into the open air leaving you with no volume. Meaning.. you're going to have to either drive the hell out your subs with a monster amp, or build/place the subs correctly in order to amplify.. (or in my case.. both

)
For a boat, I would highly recommend looking at a Bazooka enclosure for many reasons. They're a weatherproof enclosure that's tuned right to maximize sound through porting and you can mount them anywhere while "corner loading" the sound. In a runabout, they fit nicely up under the dash. Check these pictures out:
Here you can see the 12" enclosures fitting perfectly under either dash of my 18' bow rider. They fire directly into the corners of the boat and amplify like CRAZY.
Here is a closeup of how they fire. This isn't a case of your speaker or power wire or subwoofer sensitivity levels, this is just simple audio system building in a boat.
For off-brand amps, people really seem to have good luck with SSL products:
http://www.amazon.com/Sound-Storm-L...79C6/ref=sr_1_4?ie=UTF8&qid=1335536557&sr=8-4
If you want quality + marine durability, go MB Quart. Best bang for your buck by far for a marine amp. The listing is wrong, BTW.. it's a 240w amp.. not 180w. Not the biggest amp in the world, but your choices are very limited in marine when it comes to anything more than 60w per channel:
http://www.amazon.com/MB-Quart-NAU4...1?s=electronics&ie=UTF8&qid=1335536678&sr=1-1