Yeah, that "Auto Launch Apps" option is a comma-delimited list of app numbers ("1,3,2" for example) you want to launch automatically before launching a game.
One example is if you want to auto launch CPViewer to show the controls for the game right before you go into it.
Another might be to use the GPWiz49 utility to flash your GPWiz49 to the correct joystick sheme for the selected game before launching it.
That sort of this

-sab