The easiest way to understand this is think of the three boxes as a cube, the top left box is the top of the cube, the bottom left box is one side, and the bottom right box is the side adjacent to the previous box. Your selection in each box would make a line going straight in the direction of the side it's made on, and the point where all three lines would intersect is where the new part of the model will be. If anybody is interested I will try to make a video showing this.
There is a pretty large issue with the program running at however fast the graphics card can update it. The program runs at around 2500 fps for me, which is causing my graphics card to make odd screeching noises. Could you limit the application to only running at, say, 60 or 120 fps rather than unlimited? It would also save a lot of battery life on laptops.