Have a technical question you can't find the answer to in FAQ's? Ask it here. Game problem questions that do NOT pertain to things like training advice, what would my horse do well in, how much is it worth.
Same way as you put a normal dye on a horse. You have to get the dye (either make it (you can't make box dyes though) or buy it from the market) go to your inventory, find the dye, click the use button, then choose the horse you want to put it on.