When you hit TAB, go into "General Game settings" and you will see "P1 Up", "P1 Down", etc... settings which you already know how to set ... these are for Player 1 games which use one joystick only.
What you need to do is fine the following settings, which you need to set for games where Player1 uses two joysticks:
"P1 Right/Up" <--- Player1's right joystick UP
"P1 Right/Down" <--- Player1's right joystick DOWN
"P1 Right/Left"
"P1 Right/Right"
"P1 Left/Up" <--- Player1's LEFT joystick UP
"P1 Left/Down" <--- Player1's LEFT joystick DOWN
"P1 Left/Left"
"P1 Left/Right"
... you can map similiar settings for Player 2 if you have games where Player 2 needs to use two joysticks as well (Smash TV perhaps?)
make sense now?