I personally take a path of simplification. You do not need 50-100 different colors you only need maybe a dozen. I have shrunk my color selection down and have written down the formula of colors that I render with for different elements. Yes sounds boring, but we are trying to create simple graphics that convey our designs and not trying to recreate The Sistine Chapel on every rendering. If you are drawing a colored pencil drawing that is going to be shown in a gallery I understand the need for an overwhelming color palette, but for design rendering keep it simple is my motto. Then I bundle the colors by element that I use them to color, for example, my tree colors are bundled, my grass colors in another bundle.