The same set of four colors serves two independent purposes. The colors of the hexagons match groups of stitches in the thread diagram. The pair diagram has a color-code that can express unorthodox stitches.
Click a stitch in the pair diagram to remove the color from the corresponding stitch in the thread diagram. The go-to buttons lead to pages where you can highlight threads for three-pair respectively six-pair connections and replace stitches. You can save all three pages as a PDF document. The tutorial elaborates choosing stitches and has some bonus subjects like foot sides and modify or create recipes.