I've got the Bose system with the so-called sub right where the rear storage compartment normally sits. It's ok but it's no real sub compared to my previous setup with 2 JL Audios. I think it houses 2 6" speakers.
Maybe you can get creative and somehow drop at least an 8" JL in there.
Whatever you do, make sure that the box is structurally rigid. Using copius amounts of Dynamat for the doors and surrounding areas would help too (which reminds me...I still need to Dynamat my doors). There's nothing worse than a lightweight fiberglass box rattling to the music...
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