I don't think it has anything to do with being "underneath" a seat as it does with location. I placed 2 subs behind my rear seat in my 2002 silverado and they are actually touching the top part of the rubber and they sound excellent. The bass increases only slightly when I lay the seat back down. In all my experience installing subs I have learned that they like to be in a box and then pointed at something other than the listener. I can't get a good picture of what you are doing because you didn't say what kind of boat it was. I have a 268 Slickcraft and I put 2 12" compVRs in the back to back fold down seat. I positioned them to fire into the freeboard away from the listeners. You can not even see them they are on the outboard side of the seatbase and only about 10" away from the freeboard. I did this after testing with a box with 2 12s and moving it around and listening. There were lots of places where they were very weak. You don't need to have 2 subs to test for 2 subs. You can just get a small truck box with a sub in it and long speaker wire and move it around and test.
Don't worry honey, I got it on sale for Ninety bucks!