I'm using a miniDSP SHD to integrate 2.2 system (2 main speakers, 2 subwoofers) and have found that doing correction in 3 stages works best.
Stage 1 - Measure separately and work out best crossover - 12db? octave low pass and 24db/Octave in my case).
Stage 2 - Equalise main and subwoofer...