Just starting my own installation this evening and configuration I was going to try this later on
http://www.lifehacker.co.uk/2014/05/11/build-one-retro-game-console-easy-way
Edit I got both of usb snes controllers working now
Make sure you have one controller fully configured first!!
See this post
USB controller not working on Emulator
Then connect via winscp or something and
Modify the following file location is below
/opt/retropie/configs/all
Filename: Retroarch.cfg
Scroll down to this section here
<em># Keyboard input. Will recognize letters ("a" to "z") and the following special keys (where "kp_"
# is for keypad keys):
#
# left, right, up, down, enter, kp_enter, tab, insert, del, end, home,
# rshift, shift, ctrl, alt, space, escape, add, subtract, kp_plus, kp_minus,
# f1, f2, f3, f4, f5, f6, f7, f8, f9, f10, f11, f12,
# num0, num1, num2, num3, num4, num5, num6, num7, num8, num9, pageup, pagedown,
# keypad0, keypad1, keypad2, keypad3, keypad4, keypad5, keypad6, keypad7, keypad8, keypad9,
# period, capslock, numlock, backspace, multiply, divide, print_screen, scroll_lock,
# tilde, backquote, pause, quote, comma, minus, slash, semicolon, equals, leftbracket,
# backslash, rightbracket, kp_period, kp_equals, rctrl, ralt
#
# Keyboard input, Joypad and Joyaxis will all obey the "nul" bind, which disables the bind completely,
# rather than relying on a default.</em>
You should see the controller configuration for controller 1 already like so
input_player1_a = x
input_player1_b = z
input_player1_y = a
input_player1_x = s
input_player1_start = enter
input_player1_select = rshift
input_player1_l = q
input_player1_r = w
input_player1_left = left
input_player1_right = right
input_player1_up = up
input_player1_down = down
Copy it all and replace _player1_ with _player2_ so it looks like this
input_player2_a = x
input_player2_b = z
input_player2_y = a
input_player2_x = s
input_player2_start = enter
input_player2_select = rshift
input_player2_l = q
input_player2_r = w
input_player2_left = left
input_player2_right = right
input_player2_up = up
input_player2_down = down
save the file and reboot and enjoy that’s it.