If you're using GPIO for input (this may apply for the Teensy as well) and want to have a joypad connected via USB so you can have two players, you need to make a couple of edits to the retroarch.cfg file. Without these edits your connected joypad acts like player 1 and will do the same thing as the controls on the GB itself.
Set up your joypad first (press START and go to Configure Input and follow the prompts). Now exit emulationstation and from the terminal type:
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nano /opt/retropie/configs/all/retroarch.cfg
Now, your USB joypad will be considered input 0. For whatever reason, apparently the GPIO keyboard (and maybe Teensy) will be considered input -1. I haven't found this recorded anywhere, I just tried it and it worked. Add these two lines before or after the input_player1 lines:
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input_player1_joypad_index = -1
input_player2_joypad_index = 0