Great question....that was never answered. Since I am doing an Amp soon.....AND b/c I was trying to be a good boy and use the search engine.....I am Officially Resurrecting this thread!!!
I found this thread but no pictures and guys just rip the vent out? I figure you should Duct Tape it to stop the air flow and allow other vents to work more efficiently.
http://www.toyota-4runner.org/audio-electronics/25593-write-up-installing-amp-under-seat.html
I want to install an amp under my seat too, is there another write up like this one with the photos?