I guess you know how eanble one pad ("Options" -> "Ddefault game options" -> "Controllers" -> check "Enable joystick input")), then you only need to make sure the axes of both pads are enabled ("Options -> "Default game options" -> "Controllers" tab -> "Digital joystick axes": check every option there). Now you can remap the player 2 input, just start the game and press [Tab] -> configure input