Is your car making the noise? Or is it road noise? Check motor mounts and exhaust hangers before deadening. I have a 89 civic hatch with two 15's and it's quiet as hell without my subwoofers playing. I have an all stock exhaust, good mounts and bushings, ect. Oh and my car only has 1 1/2" ground clearence as well.
To stop rattles, expanding foam helped me out in the hatch, not sure how that would help you In the trunk but it's worth a try.