Heya Guywiththegun,
Welcome to EAB
Firstly what type of joystick do you have connected and secondly can you see / use this device in Windows?
Doing this from memory as at work so... Next in the "Game Ports" area you should click the drop-down list and see your joystick. Select "Port 2" and for this and that should be all.
Regarding using the Keyboard Layout A & B; these are the assigned keys:
Keyboard Layout A:
Up = <numeric keypad up>
Down = <numeric keypad down>
Left = <numeric keypad left>
Right = <numeric keypad right>
Button 1 = <numeric 5>
Button 2 = <numeric 0>
Keyboard Layout B:
Up = <up>
Down = <down>
Left = <left>
Right = <right>
Button 1 = <right CTRL>
Button 2 = <right Shift>