First thing i'd do with that prefab box is run a good bead of silicone on the inside of every corner. Honestly you are better off just making your own box so many materials and so many ideas. Then you can make the perfect setup for your install.

As for the direction of the sub it doesn't really matter face it to the back of the trunk it will bounce the sound waves of your trunk lid and the higher frequency's will be less noticible. I have mine faceing into the cabin as well I just made sure my adjustments on my amp compensated for. Just wondering why you are building the wall behind your sub? Thats a lot of extra dead weight, or are you gonna go big and trick it?