Once a pre-scan has been done there are 2 ways to add a marker:
Double click on the graph in the Measure window. That will create a marker in the Marker Table:
Or right click in the marker table area to add a marker:
When the markers are set correctly you can right-click on the marker to select Add to Peak Table:
Now when you tab to the Peak Table you see the added Peak (in addition to the Peak Search peaks that have been located if you clicked on Peak Search).
Now, in the Test menu select Final Scan Start. The final scan will update the Final Svan Levels for all the items in the Peak table using the settings on the scan config: