I went through the same questioning last year for my 88 turbo targa, and this is what I have come up with.
The targa fits right on top, with room to spare. The sub is 10" shallow mount. The downside to most shallow mount subs is that they have a hard time producing under 40Hz frequencies, and therefore the audio sounds incomplete. What people often forget is that the box is 10x more important than the sub you fit in it. Since I don't have the skills to compute audio analysis into an enclosure I would have built myself, I went with a sub/enclosure combo from Kicker. The great advantage of this is that the enclosure has been specificaly designed for this shallow mount sub. What I was aiming for was definately sound quality, and 1 year into it, I am still very satisfied. It sounds amazing with and without the targa in the trunk (a bit louder when the targa is there too).
As for my setup; no brackets on anything, carpet to carpet friction is well enough, and I didn't get to drill any hole through my carpet. I like to push the supra in corners and acceleration, yet the sub has never moved an inch. The sub + box is a Kicker
comp VT that I bought on sale at BestBuy. The Amplifier is a Kicker ZX400.1 that is fitted underneath the cardboard thing of the trunk. It does get hot, but never overheated (Wouldn't do that if the amp didn't have thermal shut-off though). If I were to do it again, it would choose a 500 Watts RMS Amp to go with my 400Watts kicker sub. The wire that is seen in the pic goes through the pre-existent hole in the carpet. It has a speakon connector, for quick disconnecting the sub. This allows me to remove the sub in ~20sec whenever I have to.
All in all, I am very happy with my setup. My supra is bone stock and this keeps the look it too.
