You don't unhook the woofer box, that is not connected to the rear decklid in any way. That is connected to the two metal brackets on each side.
You may need to remove it to unhook the rear decklid from the car. My woofer box was allready removed at the time.
There are about 4 tabs that come out the bottom of the decklid and through the meal support underneath (above the subwoofer enclosure) I don't have pictures of those anymore, but they are similar to these here you'll also need to undo.
You need to push those tabs up from the trunk into the inside of the car. After those are loose you can push the decklid up into the inside of the car. It will still be held in place by the seatbelt straps, but you can flip it over so what was facing the rear of the car is now facing the front and the bottom of the decklid is now facing up.
Then just line the bottom of the decklid with some weather stripping. The rattling is coming from the plastic decklid vibrating against the metal support underneath. If you get something inbetween the two pieces the rattling will stop.