Wait nvm figured out how to edit the key config
/opt/retropie/emulators/pifba
then select fba2x.cfg to edit
Change it too for SNES controller
A_1=1
B_1=2
X_1=0
Y_1=3
L_1=4
R_1=5
START_1=9
SELECT_1=8
#Joystick axis
JA_LR=0
JA_UD=1