I have a Rockford Fosgate R500 Prime AB Class amp, and two 10" JL Audio Wv03-4. If I run one sub it sounds a lot more clean and a lot more loud, but if I run two at the same time it just sounds really muddy and distorted.

 

Sounds like one is wired out of phase of the other perhaps? Try switching the - and + on just one. What kind of box you got?

 

They're in a sealed box