There are posts above describing the button maps needed for the controller you are having issues with. So you will need to add them into the retroarch.cfg file. Usually use the one in the all directory, unless you need something specific for a particular emulator.
Player 2 can be added right below player 1. You can do this by using the text editor nano
nano retroarch.cfg
Or if you feel more at home with a gui, you can always startx from the command line and work in there.