Un, this was one of the reasons that in your earlier M22/M40 thread I suggested the M22s, since the VTF-2 did the bass so well, and the M22s had a bit better midrange. In your present setup although the M40s do the midbass around 50-100hz well, the VTF-2 should be even a bit better in that area. So, as Steve does, I'd still suggest that you set the speakers "small" and bypass the crossover on the VTF-2. Have the sub in the corner and the woofers in the mains positioned at unequal distances from the floor and nearest walls. Yes, of course you can set "large" and use the sub cross with a low setting in the 50hz area, but I suspect that the overall result will be better the other way.
