Good luck on your integration!
As far as the auto on goes, you also might try lowering gain on your sub's amp a bit and running Audyssey again....since you seem to need a higher level signal from the avr to trigger, this is the best way to get there to maintain proper levels, or you can simply raise the sub channel level a bit (maybe you did the latter, but "raised the low frequency on the denon effect" is a bit confusing). You could just leave the sub in the "on" position, too.