Every color in your design will require a separate printing plate, set up, and will get it's own run through the press. It's just one of those facts of letterpress printing. This is why with each additional color the price also increases. This is also why crop marks on your artwork are helpful to align the colors during printing. There are some creative ways of creating a third (or more) color though. Because letterpress ink is transparent by nature, overlapping two colors to create a third is a technique often used with great results.