By some kind of deadening product. When purchasing keep in mind that the aluminum is a very large contributing factor to ridding sound and road noise so it is a plus. You can buy some kind of tool to apply it such as a roller, brayer, ect. as well as something to cut it with to match your needs on different panels such as razor, utility knife, ect. Applying the deadener to the actual inner skin of the car is best when working in the trunk, doors, hood, whatever. The rear deck should be covered pretty heavily keeping in mind that some of the bass comes through, so you shouldnt cover any large holes with the deadener. The trunk lid is a large source of the rattling in most cases so covering with more than one layer (the bad thing about this is, depending on how it engineered, your trunk lid is going to be significantly heavier than before so it wont stay open. Perhaps one day while your working on your system, it will come slamming into your head full force(speaking from experience)). But make it conform to the panels as well as possible. The trunklid, the rear most of the trunk (IMO the bass reflects off),the inner quarters, the outside of the fender tubs, and the deck lid should be focused on the most. You cant go wrong with buying a huge amount and applying it everywhere. Some of the products require heat to apply, but I personally have never used them.
This obviously isnt the textbook explaination, but it worked on my applications, I guess (I never noticed an audible difference from inside any of the vehicles, the outside does lessen however)