Well, I have full-range mains (down to 32 Hz) and have been planning to do the hi-level config with "Large" L/R and "No Sub" to drive both subs in an 'envelopment' configuration. (Room is still in process.) That would eliminate re-direction problems on those channels (combining the LFE should not present a problem since there are no filters involved).

But I don't have full-range center and surrounds. If I set them to "Small" then the phase problem is back. If I set them to "Large" the bass content of those channels is lost.

Which are you suggesting?
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