To start using this tool, you should have a .nav file that you created using the in-game waypointing tools, or one that someone else has provided you. Although, editing another waypointers map should be done with the permission of the author.

Click on the File->Open menu item to browse for and open your navigation file:

This will read the navigation file for existing Nodes, Actions, and Routes and load that information into fully-editable grids:

The default view for an opened navigation file is the "Nodes" view, but you can view Actions and Routes by clicking on their corresponding tabs. You can click back and forth between Actions, Nodes, and Routes in this manner while retaining any edits that you have made.