Wow. That sounds like a bad dream
Can you use a shop vac or something to get the water out? If not, and there's still a lot of water, I would probably drill a small drain hole under the carpet that you can later plug with a grommet. I don't know... Yikes.
Was the car parked in more than a foot of water, or did it come in the windows or something?
Make sure water doesn't get into the ECU, under the passenger side floor.