I don't think you should use cardboard for the sub enclosure...those might not hold up against your JLs...oh wait...just reread your post, you're NOT using cardboard!
I like the setup with the two subs at the side, but it'd be a shame not to show off your amps and any fancy wiring. I suggest making a false floor for it, it doesn't seem too hard at all and it would look amazing!

I still have that 4 to 8 gauge distribution block you gave me back in the day, you can have it back if you want to show it off (for your grounds).
If I had some matching amps, I'd definitely build a false floor for it. I think typically, you need more length in your trunk than height when hauling crap, no? i.e. skis, golf clubs, rather than big bulky boxes?