You should ask at the Golden Ear Forum. Many of the guys have surround systems and are using Audyssey.
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Subwoofers need to be set further away in the settings in order to time-allign them as their amps take a few milliseconds to process the signal. So, it’d be out of sync if not.
If you don’t have external subs, set your speakers to Large and subwoofer to Yes/On.
Your speakers arent full range, which is why Audyssey set them to Small, but since it’s an integrated design, you don’t want to add a crossover ontop of the one built-in.
I've found the same thing with my T1s and Audyssey. After set up, I go back in to manual mode. I change the fronts to large to use the GE crossover on the T1s. I have the LFE connected to use the T1s subs for the center and other 4 surrounds. I have a by-pass mode pre for 2 channel and found if I dial up 1 notch on the back knob from Audyssey setting, it sounds about right. Your room might be different. Then I use a SPL meter to adjusts all of the levels equally, manually. After that, I bump up my GE center XXL 1.5 db. My HT is in an irregular shaped living room, so the acoustics aren't that good.
Hope this helps.