In Big Box how do I change layout for one controller but not another?

[Bedwyr]

I run Big Box using four different controllers, XBox, and the BT modkits for the SNES, NES, and Genesis. Eastern convention has the SNES controller using the outside 'a' button but I'm thinking of wanting to change that to the western convention (XBox style). How can I do that for one controller but leave the others alone? It looks like the button assignments in BB are universal?