Incase it is not documented anywhere, the controls for the Doom emulator are translated into the SNES controls, so DO NOT try to remap them ingame, create a separate config for Doom and change the buttons if you would like to rebind them. You would change the number of the physical button in the config to match the corresponding control for the SNES controller.
D-Pad = Forward/Back and Turn Left/Right
A = Use
B = Strafe Modifier
X = Shoots
Y = Run
L/R = Strafe
L2/R2 = Change Weapons
So, because I am actually using a SNES controller, by default, I can't change weapons. So I changed my physical B to think its the X button to Fire and made X think its R2 so I can change weapons. I still use the shoulder buttons for Strafe so I don't need the modifier button.
I figured this out a few months back, but I was setting it up again today, just reposting incase anyone needs to know.