When you hover over your back peg in Expert [Manual-Score] mode your peg will turn white, if you click on the peg the above menu will pop up and you will be able to move your peg by clicking the number of points you wish to take.

The scoring menu is there to assist your opponent in seeing the points you are taking; be sure to click send to send the message after you have composed it. (Note: The scoring menu is an optional part of the game)

The numbers on the bottom row are quick links for common hands