Scale Patterns
In the layout image you can see a long yellow bar running underneath the fretboard with an A on it. This is what is known as a root bar in Fret Sage. In that image the root A was selected while having the Minor Penatonic scale checkbox selected.
Basically a user can click the checkbox of their preferred scale. And then pick their desired root on the root bar. Fret Sage will then display the notes of that scale based on that root note.
There are currently 3 scale patterns to pick from in Fret Sage.
Those scales are Major, Minor and Minor Pentatonic.
Individual Notes
Along with scale patterns, users also have two options to manipulate the notes on the fretboard individually.
One option is Multiple notes. When this option is selected then all instances of the chosen note will be changed on the whole fretboard.
With the Single Notes option selected, only the exact note you clicked on the fretboard will be changed.
Users can switch freely between these to options as needed.