I don't have a system, but usually try out a variety of colors for a figure until I like it. I have often thought that perhaps I should be more systematic, but instead end up with a random variety. The samples here skew toward purple, but I think this is less true in the book itself. For shading and gradients, many of my infinity figures are coded with \foreach loops, which make it easy to implement a gradual change in color over successive instances.