Configuration is done by editing the gngeorc file in the conf folder. You should look at a line like this:
CODE
p1joy 2,3,0,1,5,4,0,1,1,1
These numbers correspond to the folowing: A,B,C,D,START,COIN,AXE_X,AXE_Y,AXE_X_DIR,AXE_Y_DIR
I think that for most joystick, AXE_X Y and AXE_X_DIR...