I have the premium DSP sound system CD changer etc...and I replaced the rear speakers with a pair of Boston Acoustics. I did this because I thought these were the source of the vibrations I would hear at high volume. The guys at the Good Guys electronics store didn't know what the hell they were talking about. The installer didn't even know that the grills pop off!!! He told me they would have to do MAJOR work to change the speakers. Please don't waste your time with these unqualified "good guys". I asked them if the system has a subwoofer and they said "NO". I figured that the vibrating was from the heavy bass so maybe it was coming from a subwoofer. Then I come home and see this link http://www.nextmill.net/bmw540/ which clearly shows that I have 2 subwoofers. I want to get rid of the rattling vibrating sound that I hear that I believe is coming from the subwoofers. What should I do? Can you change the subs and get better ones? Can you disconnect the subs altogether? Anyone out there who has modified their sound system in a 540 please respond. BMW DSP Woofer System

I am the one that documented the DSP woofer system on my Nextmill site.

In the left corner of the box is a connection to disconnect the subs. You can remove the liner from the trunk, and then in the left corner you'll see the connection, just unplug it and see if your problems go away. Is your car under warranty??? If so you might have your BMW dealer replace the DSP system. Its possible you have a bad woofer. Else you might just pull the whole unit out and take it apart and see whats vibrating. Its a NOKIA bandpath enclosure.
Other options is to completely disconnect, build a small 1.25 cu ft sealed enclosure against the back seat and place a nice 12" Kicker Solobaric inside, then mount an amp on the back of the box and wire it into the high outputs from the old sub connector. Make sure you pick an amp with HIGH inputs. This would be pretty cheap, resolve your DSP woofer vibration issue, and give you more HEADROOM in your trunk.
I plan to go to a higher extreme, running a 5/6 channel amp to the inside 8 new speakers and 1 Kicker 12" solobaric firing thru the back seat (1.25 cu feet).
Another person, Chris I believe, on this board, did the same thing. His pictures are on a post from a few days ago. You'll see that it doesn't take up any trunk space.