Well, I do have experience with this situation. I used to have a 93' Celica convertible and wanted a bassy system in so I had to compromise. I gave up the trunk and built a box that took up most of it. It was a horizontal box though so I could still use the trunk for smaller things to lay on top of it. It was a mix of fiberglass (which I didn't do myself, I had a friend who did fiberglass do it for me, we have a tutorial by Franklin in the forums if you want to learn). The box's airspace came from the wheel-well where the spare tire was supposed to be, lol, so there is always a compromise, but the airspace came out to just a bit more than the recommended for those subs. Pics below. It actually did sound phenomenal, so facing the subs upward thus far has sounded better than any other arrangement I have tried, I recommend that route if you are giving up space anyway, that way you keep your backseats and your system is invisible. You will lose alot of bass no matter what you do though because of the convertible top, but the fiberglass and wood combination box is really the way to go if you want to make up for it, the combination of flexible fiberglass which worked a little like a passive radiator and the rigid double layered MDF top makes for a perfect enclosure for crisp sounding thunder. Another thing you can consider is high-end treble, separated mid range, and use some fairly small subs that can be mounted in your rear side panels (you will need to build small enclosures for them though, done this too and it works pretty well), I would recommend Morels for the large/mid range, they are power hungry but they are devils. Look into adding an EpiCenter pre-amp to the midrange speakers to fine tune your mids, it is a fantastic device and works wonders. Then, you can skip the subs and use
bass shakers instead. In a convertible, since you will lose much of the bass at highers speeds anyway, these make a great space saving solution and actually improve your sound since it's not your ears that make the bass experience anyway these things trick your mind and in the end it ends up sounding just as good. I was surprised actually when I first heard a system that used these, just like any other high bass stereo than boomed along. You mount them under the seats so once again, invisible/concealed and you don't need to give up any room in the car. I would not recommend building a large box in the backseat. For one, your car looks tacky, two you lose seating, three your stuff is right out in the open just begging to be stolen, four your sound sucks because placing subs that close to you always sounds distorted. The bass coming from your stereo has more to do with the enclosure and the room you're in than the actual subs, the resonance from reflecting off surfaces and the flexibility of the enclosure are like a fine tuning mechanism and it's hard enough to get it just right with all that space to work with, but when you eliminate all of it and try to rely just on the subs placed behind your head, you will regret it.