Move the mouse cursor over the checker you want to move. If you now click the left mouse button, the checker will move the pips of the left die. If you have already moved one checker, clicking on a new checker will move it according to the pips of the remaining die. If you click with the right mouse button on a checker, the checker will move according to the right die.
Using this method for moving the checkers can be really effective. Some users prefer showing the higher die to the left. You can make GNU Backgammon show the highest die to the left if you choose Settings -> Options... -> Dice and check the check box labeled Show higher die on left.