Yeah, I have a 12" sealed enclosure with my Infinity Kappa sub. I kept the entire system stock, but just added the amp and subwoofer.
You're right, the decklid is very annoying and rattles when you hit a certain bass frequency. I've tried looking back there to see if something was loose, but I just haven't had the time to really look into it. I'm sure dynomat would work, but it may be as simple as bending some tabs or something. There are some threads about it, I believe.