I believe the two in the 88 are the ones by the rear stut towers (obviously both have the ones in the doors). The additional two would be in the shoulder area of the rear seat side panels. The other difference is that in pre 89 cars, the seatbelt for the rear seats comes out of that panel on the lower side (about 8" foreward of the seat backs), whereas on the 89+ cars it comes from underneath the panel, at the point where the butt pan meets the back. I'd guess this was to give a little more clearence for those speakers mounted in that panel, so that the belt strap doesn't hang over the speaker all the time. In my case, I have modified 87 panels with 6x9's, the seatbelt comes out in the stock location for an 89+ car, but it still doesn't quite clear the 6x9's very well, so I keep them buckled in.
i have an 88 and it's 4's in front, although you can cram 4.5's if you're slick. i made fiberglass pods for 6.5's in the front and cut the hell out of my door panels to make them fit. the 90+ supras had 6.5's in the front, and the 6.5 "box" (it's not much of a box) fits in the 88 doors (i have them there now) and they are a good base to construct a larger speaker box from. if you have shallow speakers then they'll fit right in tho, so measure the thing first. watch your window clearance also if you're building your own.