In the top left corner, are the current root notes on the guitar. It defaults to Standard Tuning
If your guitar is tuned differently, you can click the button to Change Open Notes. It will display a dropdown list for each string. You can change it to your tuning. You also have the option to make this your default tuning. This will allow you to have that tuning the next time you open the page.
The grey colored circles on the top of the neck are your current root notes (standard by default). If you made any changes to the Current Root Notes, it will be reflected here.
The next step is to select a root note. For example: If you want to see the notes of an A major chord, you would select A as your root note.
Next select the scale or chord you wish to see.
In this example, we selected A major.
This shows the name (notation) of the chord
This shows the notes of the selected chord/scale.
This is the legend, telling you the color of the intervals. The major chord is a (root-3-5) formula. The root is A, the 3rd is C# and the 5th is E. These colors are reflected on the fretboard.
If any of the notes of the selected chord/scale are open strings, they are displayed below the grey (string) root notes. The are color coded like the other notes on the fretboard, This is to denote that these notes are included and can be played.
This application shows you ALL the notes, all over the fretboard. It does not just give you the notes of an open chord. It also does not tell you where any of the chords are. This is by design. This tool gives a visual representation of all the notes, and allows you to find chord formations outside the usual chord formations. It does show you the open A major chord. But it shows you multiple options for an A major. Any combination of the 1-3-5 (A-C#-E) is an A major chord.
This shows 2 (of the many) options to form an A major chord. The standard open A major, and an A major on the E, A, and D strings. Both are perfectly legitimate A major chords because they fulfill the 1-3-5 formula.
This should help to get you started on finding new chords and scales.
I hope it opens opens up new scales and voicings for you.