To copy a waypoint into the scratchpad, click on the Left LSK beside it. That waypoint will now appear in the scratchpad. Now you click on either the Left LSK beside the 5 blank boxes (if you are filling a route discontinuance), OR you click on the Left LSK beside the waypoint that you want to move it to and replace.

Be aware that when you move a waypoint further up the list, all waypoints between the replaced waypoint and the moved waypoint are deleted/removed from the plan! Luckily, it does not take effect until you press the EXEC button, and the <ERASE at LSK L6 is available to undo the move/changes.

Hope you understand the explanation. If not, I'll show you using images.