Not so. Equalization will be applied to both identically by Audessey. But the time delay (phase) is set individually for each output. You want them to be time aligned to each other and to the main speakers prior to application of EQ. Can't time align them to each other if both are run off the same output. Unless they're sitting on top of each other, of course.
Edit: With the exception that you could if the subs had variable phase settings and you adjusted phase manually. I was referring to having the receiver do it all.
Edit: With the exception that you could if the subs had variable phase settings and you adjusted phase manually. I was referring to having the receiver do it all.