12" sub box...custom

well i had the same problem you did. I didn't want to remove the spring things that make the trunk open. what i did was i mad a box that went allt he way up to the rear seat and came back to where the trunk opening starts nearest to the rear window. then i built an baffel out of 1/4 in board and carpeted in grey like the trunk and made it fit so it looked like a fake wall i had to cut notches in either end so the trunk mounts would tuck in when the trunk closes. I try to get a pic its hard to describe. Since there is only about 10 inches from the bottom of the trunk to the top of those bars that assist in opening the trunk i had to make a very long rectangular box to fit in and to acheive the air space the sup needed. As far as your 2 boxes for your 6.5 componens i would either put those in your seat delete if your going that way or enlarge the holes in your deck so you can build another baffel to hold the mid-low and your tweeter in the same unit.
i hope that helps a little but its very hard to explain let me know if there is anything else that could help you.

in an emergancy (flat tire) you are able to take down the fake wall (baffel) and pull the sub box out to remove the carpet and get to your spare. I inverted my amps and mounted them upside down under the rear deck.

You can look at my garage to see what sort of equipment I am actually running. I was able to get two 10s in a downfiring box that slides under the spring rods. I mounted the amps to the front of the box. That way you can just fold the rear seat cushion down to "service" the amps if needed. I have pretty decent size 10s too so depending on the size of your 12s it shouldnt be a problem. I used to have the plans for my box around if your interested.

On the left you can see the box I made. The rest is basically for show. The top styling plate I made extends a few inches past the actual box, and again is just for show to clean it up. So with the box alone, it leaves more open space if that's what you're looking for.

You could just as well mount the amp underneath the top well, and keep the rest for storage. The backing plate you see in the pic pulls right out, and I have a little storage room available should I need it.

It all pulls out in a couple minutes so I can access the spare tire, too.

Before I did this I had just a simple box that I left in the middle of the trunk, leaving me about a foot wide on each side for storage.

Or you could build a simple, thin box and stuff it under the top well completely. You can find a shallow fit 10" to work, but I doubt any 12" will fit. Or three 8" woofers could work too, provided you give it adequate space it will still BOOM very well.