One thing I noticed, even though it's only a 200 seat black box, the 5.1 effect is highly localized. So it'll sound great to a half a dozen people but will be completely lost on the rest of the room.
What is the speaker setup? What is the assignment of the speakers to the DSP channels when in 5.1 mode?
Are you using a home DVD as source? It was probably remixed for home 5.1 etc sound. Movie theater sound systems have multiple speakers fed the same signal for surround left, right and rear channels.
You are getting into the deep end again on sound. The The Recording Academy's Producers & Engineers Wing Recommendations For Surround Sound Production describes several of environments used for surround sound and is the right price at free. Another good reference on movie theater speaker systems (and still free) is the JBL CINEMA SOUND SYSTEM MANUAL. These are in addition to the excellent documents SHARYNF linked.
Andre