oh-kaaay, frequenz, listen very carefully, this is how to read it:
In the diagram you can see two representations of the guitar neck. One is the 12 fret view and the other is the 24 fret view.
The 12 fret view (top) has indicators below that show the fret numbers - III, V, VII, IX, XII (3, 5, 7, 9, 12).
ON each neck there are six parallel lines representing the strings. The topmost one (the one nearer the top of your screen) is the high (thin) E string. The bottommost one (the one nearer the bottom of your screen and your keyboard) is the low (fat) E String.
A red dot indicates a chord tone. For example, if you have the tick in the 'chord' checkbox and have C major selected, you'll see all the notes C, E and G lit up on the entire fretboard, showing all the possible combinations of those notes.
A black dot shows the scale tones, i.e. all the notes in the particular selected scale.
The tool is meant to help you learn all the positions of the notes in the scales and chords. You can turn on and off scales or chords when you want to concentrate on certain aspects, for example, if you are learning how to play over changes, you might want to turn on just chords, so you can learn to land on the correct notes of underlying chord in a progression.