Mark your waterstone with pencil marks using a soft led pencil with an "x" or grid. This will allow you to quickly see if you have removed the entire top surface of your waterstone.
Soak both the waterstone and the Naniwa Flattening Stone in water. About 30 minutes is best depending on the type of waterstone you have.
Position the Naniwa Flattening Stone over your waterstone and using the weight of gravity move the stone backwards and forwards to remove the high points of the waterstone. You may also use a figure eight motion. Keep the stones wet. If possible do this under running water.
Continue until your stone looks fresh and clean with the pencil marks removed.