This is what I have found works best for both the Supernova, as well as last year's Kook Pro Players duffle.
The logic I use is that when I pad up to bat, I should be able to do so without taking everything out of the bag first. And so this is what I ended up doing in the main compartment:
Helmet at the very bottom, straddled by my batting pads (I only have one pair). I also slide down my chest guard (not used in games) and have it "hug" one of the batting pads.
Elbow guard, gloves piled on to the helmet.
Next come the thigh guards....resting on the two top hats of the batting pads.
Box on top of thigh guards.
So, when I pad up, I just open the top flap, and go about it (box first, then thigh pads, etc, etc, helmet at the very end).
Everything else goes around this basic concept. One side pocket is the dedicated "infrequent use" pocket, and has spare stretto fox straps, medical stuff, etc.
All other stuff (whites, socks, shades, balls, etc) gets distributed in the other pockets and shoe tunnel (I also stuff a few balls in the shoe tunnel).