If you want to see what points are being used by the coloring IFS and where they fall on the input image, check the box "Show Points". You can click on the colored square to change the color of the plotted points. This has no effect on the colors used to plot the drawing IFS fractal. By default the coloring IFS will be scaled to use as much of the input image as possible.
If you want the coloring IFS to be drawn so that the horizontal and vertical scales are the same, check the box "Equal Scale". This may change the colors used to plot the drawing IFS. Compare the image below with the first fractal drawn above.