For those of you that have a similar water issue in an e30 convertible, the drains for the well into which the top folds when you put it down are near the hinges, towards the outside of the car (on both sides) and aren't visible because there's some wires and cables in the way of seeing them. I just made a coathanger "tool" and felt around with it until it went in the drain hole. Note that the holes aren't on the botton of the space, they're on the side of it. They drain into the sills, which drain out of the car. I moved the wire around a bit and out went the water built up over two days of rain.
I'm verry pleased.
Shout if you need photos. :p