that is a very common problem on the hatches. What it was for me and many other people was the rubber gaskets that surround the left and right taillights. They are made of butyl rubber which starts breaking down around 8 years or so. There is a pretty good write up on how to fix it at
http://www.240sx.org/faq/index.html, look under "water leak." Wasn't too bad, took me about 3 hours and I wasn't really working the whole time. The spare well already has a drain hole, if you take the tire out it is in the well towards the front of the car. It is normally covered with a black rubber plug. I just took the plug out before I fixed the problem on my old car so the water wouldn't accumulate.