Actually, I updated the layout in version 5 based on user feedback, and keep it in version 11, Rex's is from original manual and I need to update that.
Axe-Fx III Manual says Output 3 is designed for sending to Power amp and real cab (set the output knob to max). I put a GEQ4 block in front of it so you can tweak it at that GEQ4 to cut/boost lows/highs/mids to tailer to your system.
Here is what a Naked Amps preset layout looks like for version 5 to 11+:
(Note some presets may have more effects in them than shown here... things like phasers, tremolos, chorus/flanger and detune etc are preset specific).
View attachment 61554
So the idea is:
Out1 - main out, to FOH and/or stage monitors
Out2 - secondary main out, in case you need to split monitors out from FOH out. You can mirror Out1 to Out2, or use Global GEQ to adjust Outp2 if to on-stage gear. You could also use this for In-ears
Out3 - for power amp/cab. This does tap directly off the amp before the cab and any wet effects, so it is not going to sound like I designed it exactly (cabs are half the sound) but it IS a built-in option and you can use the GEQ4 block on a per-preset basis to adjust for your own power amp/cab setup
Out4 - extra signal out, could use for In-ears.
It seems to give people the most flexibility.