hey mate,
I am going to hit this problem in the future, luckly my installer, knows a few tricks. first I am getting sound proofing put into the boot lid, plus new carpet
Also the two parts of the boot that are most likely to start, are of course, a lose number plate, can be fixed by a thin layer of either carpet or sound proofing size of the number plate.
second is the cheap rear wing break light, this will also make a rattling noise along with the rear wing itself, if you tap the rear wing, and I mean only slightly then you can see outside what is causing the problems. if you pad the break light then I would say you will have removed most of the rattling noises of the exterior of the boot.
As for the interior, check cables with plastic pieces, either tape them or above put something in between to lower the noise created, also dont confuse boot rattle and the sound of the subs air pressure push hitting the panels(bad is high pitched i think, good is low pitched rattle), different sound and the second is the sound you want not the first one.
rattling = sounds like really shotty poor job
panels vibrating = good sound, sounds tough.
My flat mates commodore, has 2 kicker comp subs, hold the number plate down and you get the awesome sub rattling the side, with no stupid number plater rattle.
my car will have 2 type-r's so I am going to look at everything possible to get it sounding right.