If you use the registration color for these marks it will show up on each separation without having to change the color. When printing screen-printed separations, you can add your own custom registration marks on the page so you can control where they are on the output. They are labeled with a name, so you know exactly which separation or color plate you are printing. Think of it like a coloring book and each color crayon you color with or use from the spot color palette is a separation.
In some printing processes that use spots color, like screen printing, you need to isolate each color into individual color areas so they can be printed on the same plate or screen.