I would also like to suggest that every audiophile should have a calibrated measurement microphone and program. You will never know what your system is doing unless you measure it. A good program will also give you group delays which will allow you to integrate the subwoofer better.
It is also important to note that the low pass filter supplied with most subs will never integrate a subwoofer to maximal effect. This requires a complete 2 way crossover preferably digital with room control and delay capability (digital bass management)
Removing the low bass from the main speakers increases head room and lowers distortion. It is like doubling the power of your amplifier.
A proper sub system is a set it and forget it item. I use my system for theater also and I never change settings for theater. The proper adjustment is proper for everything.