I also have a question dealing with this. I have a 12" w3 in my focus sedan. What I was led to believe is that it will be louder if facing backwards, because the bass will be able to travel more, but my real question is thus: I get some lame trunk rattle, would it stop, or lessen if subs are facing forward?
I think your best option is sound deadening. Its easy to do, and has a great effect on your sound. You could probably do the whole trunk with 30 bucks. Check out edesignaudio.com their eDead is very reasonable, and it works very well.