I put a deck mounted sub in my E39 and love it. The additional amp was installed above the battery and the sub mounts directly to the rear deck lid. Clean install and super sound!
2003 530i Titanium Grey/Black, Premium and Cold Weather Package, Ultimate Pedals, iceLink iPod Kit, Bluetooth, M5 Deck Lid Spoiler, M5 Rear Sway Bar, M5 Dead Pedal, DINAN S1 Trans and Engine SW, BSW 12' subwoofer, Valentine V1 hardwired, SMG Paddleshift kit
2005 X5 Sterling Grey/Truffle Brown, Premium and Cold Weather Package, DICE iPod Kit, Bluetooth, DSP, Comfort seats, Invision DVD Headrests, Valentine V1 hardwired, TomTom GPS