Sounds like water is getting in around the clamshell and the drains under the convertible top are clogged and overflowing into the cabin. The hardtop doesn't cover the back edge of the clamshell. This is the most common source of water under the seats, a quick search will pull up diagrams, instructions on how to clean the drains, and the part numbers of the 987 drain covers you can install to keep them from getting clogged again.
