@rmiller6 If the scenario is exactly what you described and what you want is
player1 = keyboard
player2 = joystick (the only one you have plugged)
The only thing you need is edit /opt/retropie/configs/all/retroarch.cfg and look for the lines with input_player1_device_index (same for player2), remove the comments and do the following:
input_player1_joypad_index = 20
input_player2_joypad_index = 0
The index 20 is a high and inexistent joystick (who has 21 joysticks connected?!) and it makes the player1 unplayable via joystick, only the keyboard controls it.
The index 0 for the player2 is the first joystick connected.
This isn't the only way to achieve what you want, but I can assure it works. I've just tested here before posting.