There are various U.S. and international regulations with opinions on how to best annotate your master document, but no one way. Whatever method you choose, you should be able to explain it if an inspector ever comes knocking on your door. The method shown here has served many well for all these years...
What follows comes from the references shown below. My techniques are shown in blue.
[AC 91-70A, ¶3-5.b.]
NOTE: Some operators use a diagonal line approaching a waypoint to confirm a subsequent waypoint to include coordinates, track, and distance.
[NAT Doc 007, ¶ 8.2.7.]
The waypoint or waypoint number (for aircraft LRNS requiring numbered waypoints) is circled to indicate that the course and distance information has been compared to the plotting chart and its database coordinates have been checked.
A diagonal line will be drawn through the circled waypoint to show that the course and distance displayed in the FMS has been verified against the Master Document and plotting or en route chart.
Following acknowledgement of the position report, a second diagonal line will be drawn through the circled waypoint (creating an “X”) on the Master Document to indicate these duties have been completed.
Portions of this page can be found in the book International Flight Operations, Part VIII, Chapter 39.
Advisory Circular 91-70A, Oceanic and International Operations, 8/12/10, U.S. Department of Transportation
NAT Doc 007, North Atlantic Operations and Airspace Manual Doc 007, Edition 2013