Water drainage

Short story here: I've got the rear seat and rear side trim panels removed from my 63 wildcat convertible. Couple small holes to fix, sound deadening, super cleaning.... While washing the outside of the car I noticed the water going between the top and back glass and disappearing to what looks like the interior of the car. I go inside and there it is, dripping into that 3 X 3 or so space behind the mechanicals for the top. It was a couple inches deep before it eventually drained away. This may all be correct, ( I am very new to the ragtop scene ) but boy, does it look like the potential for a rot disaster. The small holes I am fixing are under the back seat near those corners. Everything in this area is still intact and pretty solid (definite surface rust though), so it seems I've caught this in time but any advice on what to do before I put the finish back in? Is this really where the water is supposed to go?
Thank you
Tom

 

Convertibles have a drain channel around the base of the top where it goes under the sheet metal. You can see it if you're lying in the trunk looking behind the well liner. There are tube drains that connect at either side to take the drainage from that channel and direct it to the space where the top pistons are mounted. On the inside of the rear rockers, there is an opening with a rubber flap (you need to be under the car looking outboard to see it) covering it. That's where all the water from the drain channel leaves the car. Or is supposed to. I've had 3 convertibles and every one of them had debris inside that plugged the drain flap, and yes, it's a prime location for corrosion. That's why you take whatever steps are necessary to keep that area clean and dry.

 

And there it is! Thank you Joe. That is the answer I was looking for. I will clean it, get it working properly, paint it all with rust shield and keep water away.... As much as possible at least.
This forum is so awesome... Lots of knowledge out there.
Thanks again
Tom