Audyssey doesn't know there are two subs, only you (and we). So, the general concensus on a dual sub configuration in a 5.1 system consists of the followings:
1. Place the subs to equal physical distance to the MLP (Main Listening Position).
2. Adjust gain knobs on both subs equally.
3. Run Audyssey auto setup.
As to your query on both subs firing during movies, but only one working during music: no idea, actually than shouldn't happen! Check again, please!