Having been a member of the "Boom Boom" brigade back along (until some nice boys from the local estate stole it all) my advice would be.... ideally on a Sunday morning at about 5 am after about 8 pints of stella the nite before, get the system warmed up (5 mins on normal volume).
Lower the back seats (if they move, not too sure about such modern machines) crank it up till it rattles but leave the boot shut. Crawl in and press everywhere until rattle is traced, removing trim etc until you find the source. If seats are fixed, get in boot and have responsible mate shut you in to repeat the above.
Also check back number plate, my BMW one used to fart like a grandma with drum and bass pumping (the plate, not the grandma) and the jack, wheel brace, and spare wheel and its mounting gear. Also worth checking is the connections to the back lights, if on big clip blocks a few inches back from the lights they can dring on metal beside them.
Should the rattle be the sub cone or mag its self, new really powerful replacements are so cheap now that you can get a new un and develop new interesting noises/rattles within hours of installation.
Dynamat is cool and really works. MY VW Bus was loads in it but alas no tunes due to the wankres back in 1997, when I lost interest due to no insurance for the gear £2K was alot to lose then..
Happy hunting for the rattle and remember.... heart thumps when bass line pumps!!
PP