If you are using minidsp and two amps the equalization need only be applied to the woofers. Then the question remains whether it involves boosting the lower frequencies, with the problem of accentuating any noise on the signal, or reducing the upper to mid bass, to arrive at a flat response curve up to 45 hz.
Rick,
Do you have any feel for how minidsp will perform this task - will there be a lot of audio degradation?