You're probably getting a boomy sound because it's traveling right up through the med kit hole. Try facing the subs either towards your back seat or the opposite way and see what kind of sound you get. And I read on the JL website that a box built with a port is less boomy, so you might want to read this, it was pretty helpful:

http://www.jlaudio.com/tutorials/magic/index.html

Click on the links above the text "Sealed boxes" and "ported" and you decide what sound you want best