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...
Everything here is from the references shown below, with a few comments in an alternate color.
[AC 91-70B, ¶188.8.131.52] Adopt an appropriate symbology to indicate the status of each waypoint listed on the master document. For example:
[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.
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