Actually I use my Neo geo config like this
B C D
A x x x
Because if you look at any pictures of actual Neo Geo joysticks *like the kind for the console Neo Geo* you'll see how damn much of an arc there is on the A button for your thumb. If you look at my CP picture up above, notice that the A Neo Geo button is almost lined up with Button 4 in the bottom left corner, that's because I put my hand on the controls when I was designing it and I just marked where my thumb naturally rested, and there ya go.
If you're really into the square button layout, then here's what I suggest if you're a Neo Geo fighting game fan
A C X
B D X
A=wp, B=wk, C=hp, D=hk. yesss... for samurai showdown though, the thumb layout works the best for me., and you would not believe how much easier A B C is to push for KoF games to initiate your super bar, and charging and such.
-Good Luck
-Chu Chu