Audyssey and Tritons

You should ask at the Golden Ear Forum.  Many of the guys have surround systems and are using Audyssey.  

Yes...good idea.

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.

The GE Triton Ones are definitely full range.  

@stereo5 

True full range means they can achieve 105dB at 20Hz in the seating position, which they cannot do.

Perhaps not by strict definition. But they produce more prodigious bass than anything else I've heard. Including standalone subs.

@secretguy  
  
Get a pair of Rythmik FV18’s and report back ;)

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.

mzkmxcv...sure. I'll go spend another 3800 to get what I already have.

12blistn...I haven't had time to mess with it. I will do a manual tweak soon.