Hey so I really only made an account to respond to this query. The easiest way to deal with this is finding the .cfg file for the PISNES emulator. PISNES searches for a different cfg file than the built in emulator (so you need to manually edit it for each different controller) where as the included emulators reference the cfg file you set up when you mapped your controller the first time you connected.

Remember when you had to first set up your controller? You need to know what each button corresponds to Go to the MAIN MENU and hit Configure Input Notice that every time you hit a key while mapping a number appears? You'll want to make note of what number each key is Connect to your Raspberry Pie via SFTP and find opt/retropie/configs/snes Notice there is a file in the directory named retroarch.cfg - that's file contains data helping built in emulators You want to open snes9x.cfg (this is what PISNES uses) with a text editor Scroll Down until you see this!
[Joystick]
A_1=1
B_1=0
X_1=3
Y_1=2
L_1=4
R_1=5
START_1=7
SELECT_1=6
QUIT=99
ACCEL=98
QLOAD=10
QSAVE=9
#Joystick axis
JA_LR=0
JA_UD=1
#Joystick DPAD buttons
LEFT_1=11
RIGHT_1=12
UP_1=13
DOWN_1=14
#player 2 button configuration
A_2=1
B_2=0
X_2=3
Y_2=2
L_2=4
R_2=5
START_2=7
SELECT_2=6
#Joystick axis
JA_LR_2=0
JA_UD_2=1
#Joystick DPAD buttons
LEFT_2=11
RIGHT_2=12
UP_2=13
DOWN_2=14

- These are the original values! Values corresponding to keys will change depending on what controller you are using

Change each value to the appropriate value of the corresponding key you want (the info from step 1)

Profit

PiSnes controls are off.