Problem with water getting inside
 

I just bought a 99 boxster, great so far but today I noticed that i have a lot of water behind the driver and passenger seats. The carpet is drenched behind the seats and no water anywhere else in the interior. Its not the top I checked that first. Any ideas?

If the drains are clogged up that's where water will end up. I had the same problem on my97 on the passenger side only. It is hard to understand how water gets to that point, but that's where it goes. You can test with a water hose and watch for water running out the drain holes on each side. They should run freely right through as you run water down the top. You should be able to search on the problem here or on Rennlist or pelican. I can't recall which forum I used at the time.

take car of that pronto.
vital electronic components reside under the seats.

There is a plastic apron under the clam shell that covers the engine cover. It has a rod that goes across the back edge of it, that should be clipped to the firewall in 2 places. If that apron isn't in place, it won't direct the water that drips down, into the drains. The clips can get broken easily if you forget to undo the apron before you put the top into the service position to access the top of the engine.