I will be putting a layer or two of sound deadener on the rear deck.

Is it better to remove the stock subwoofer and have an open hole, Keep it in there or Remove the subwoofer and put something like a piece of MDF over it and sound deadener over it?

 

if you are adding subs to the trunk then remove and deaden around it. If you are not adding subs and trying to eliminate sound from the trunk cover and deaden the hole. I like 1/8 abs or 1/2 mdf deaden the hole and use factory hardware to hold the cover down and then deaden.

 

I have a sealed box in the trunk. So I guess I'll remove it and work around it.

 

Removing it will let a bit more sound to pass into the cabin