It looks like you may have only configured the controllers for emulation station and not necessarily the emulators themselves. Floob has some good tutorials on how to do this: http://m.youtube.com/watch?v=OBloKEbBRAU
I have followed that video and in fact did do that (register the USB controller)
The issues I get is I’m as the screen when it says please make sure only the USB controller is plugged in, I press enter on the OK then it goes straight to the window telling me the file has been saved it does not give me the window to press the button to config them.
Before that window comes up I do see for a second the black window that I assume is the one to enter the button presses.
Any ideas what I can do now, even tried it with no keyboard plugged in but of course I have no way to press enter not he OK
When I configured it I used ssh to start the program and then once it told me to enter the keys I used the controller, even though it wasn’t showing on my TV screen what was happening on my computer it would still register the joypad buttons.
You can also change the controls manually:
sudo nano /opt/retropie/configs/all/retroarch.cfg
This shows an example of where to add the joypad configs: