There are two different ways to draw invisible lines, using the Pencil tool or Stroke tool.
Using the Pencil tool, you can draw as strokes only, meaning that the line will be invisible. This can be useful for drawing tones and highlights directly on the character.
The Stroke tool draws invisible lines only. You cannot add thickness to the line. Unlike the Close Gap tool that creates a short, straight line between two points, the stroke line will stay exactly where you draw it. This tool can be useful for closing a zone in a particular way or creating some hard shadows or highlight areas.
Sometimes, it may be difficult to see strokes, especially if your colours are similar to the blue stroke colour. In Harmony, you can display the strokes in washed-out colours so the invisible lines stand out.