OK I will admit, I don't make cookies so my advice is strictly based on the books I've read and experience specific to cake, BUT, what kind of recipe and what kind of colors? The recipe above calls for water - I never thin with water, ONLY fresh lemon juice if I need to thin but that doesn't happen very often. The acid in lemon is essential to help strengthen the royal for what I use it for. But I am careful not to make the mistake of making my royal it too stiff then adding lemon juice to thin then adding powder sugar then adding a liquid and so on. If my royal is too stiff I add another egg white and powdered sugar and just make more royal.
As for adding color, I use gel or powdered color, powdered if I can help it because even if the color pigment sticks the extra liquid in gel can throw off and make a puddle like you said. Yes you mix a little bit once you take the towel off but you are right, the longer and harder you mix the more air. Your best bet is to make the icing the right way the first time and that takes experience based on whatever you are using it for. I think Sweet Ambs, although I have never paid for her icing recipe, must be making it perfect because her cookies are extraordinarily beautiful and her recipe could quite possibly be contrary to everything I just typed, but I've never seen any of her cookies that have that take-tell crater of a popped air bubble from improperly mixing the royal or using the incorrect ratios for what she does. Anyway I highly suggest HER advice as a master of sugar cookies. Google her.