I have a setup in my back panel like you're describing, with a 10" JL audio 10w3. I had it custom built by a shop when I got the rest of my setup.
The shady folks at the shop originally told me that they would keep the compartment intact and build a fiberglass enclosure that would fit inside without having to cut it, and that it would sit flush with the rest of the panel. Instead, they ended up cutting out the compartment without consulting me about it first, and gave me the wood enclosure that you see in the picture below. If I would have known they were going to cut out the compartment, I would have told them instead to keep it intact, and just extend the box out an extra few inches and have it rest on the floor of the trunk area. Needless to say, I was pissed... but it sounds great, and it gives me more than enough bass for the kind of music I listen to.
So you've got a few different options to choose from .
1) Cut out the compartment and go with a setup like mine.
2) Get a shallow mount sub and possibly be able to fit it in the compartment with a fiberglass enclosure.
3) Go with a JL audio stealth box or build something similar. They look nice, and from what I heard, they sound nice, but it'll run you about $600 and comes with a subwoofer (you can probably build something similar or have it custom built)
http://mobile.jlaudio.com/products_stealthbox_detail.php?fit_id=1421
http://www.crutchfield.com/S-Pp6gxOUuzFE/App/Product/Item/Main.aspx?I=13694021
4) A company called Q-logic makes something similar to the JL stealthbox, but i heard it's not as good, quality-wise and doesn't sound as good. Costs about $200 for the enclosure only.
http://www.audio-n-more.com/Merchan...code=ANM&screen=PROD&product_code=QL-C1T4R110