i have a 12" alpine type R in my trunk, and it rattles the rear deck of the car really bad.

how to i get rid of this? I think its the third tail light, because i put a shirt under it, and it got better.

There's your fix. It's simple, took less than a minute, and nobody will ever know. I stuffed paper towels.

 

so more shirts and paper towels around the rear deck should fix it?

 

Maybe.

http://www.8thcivic.com/forums/audio/40279-sedan-rear-deck-removal.html
You can follow this DIY if there still rattles. I put some foam weather stripping under the rear deck plastic panel wherever it touches the metal.