I did some surfing of the 4311 thread and it does appear to calibrate the two subs independently, at least the level and distance. It then, as I understand it, applies filters to both subs as if they were only one - after distance and level matching them both. So it would appear it's an ad hoc sort of thing.
It also looks like Denon skipped a model year due to the earthquake in Japan and they will be releasing the 4313 this spring. I may just wait a couple months and see what the 4313 brings to the table.
JB: Thanks for link. I did read that thread for a while, years back, but got lazy. It's too much like reading instructions.... But ya, you're right and I should get caught up now that I'm looking to move to today's tech.
