If you wish to use a joystick or gamepad with Splinter Cell, you can only do so if your Joystick / Gamepad has software that allows you to assign keyboard strokes to movement and buttons. Contact your controller manufacturer or the documentation that came with the controller to see if you have the ability to assign keystokes to movement and buttons.
This is possible through the use of the controller software and not through Splinter Cell.
For example, if you have one of Microsoft's Sidewinder line of controllers, you can use the Sidewinder software to assign keystrokes in the following manner:
You remap the keys on your joystick in the games remap keys section of the options screen. In remap keys section, select the action you wish to assign a button to, click on this action with the mouse, then hit the button to which you want to assign an action.
If your joystick includes software to map keys to the buttons and directional pad or Joystick movement, this is most likely the best option. NOTE: before trying this, check your joystick / gamepad documentation to ensure your controller has this ability to assign keystrokes to movement and that you are able to change these configurations.