Color! It's something that Manga Studio in the past has been criticized over. Previous versions of Manga Studio concentrated on black-and-white and grayscale art and weren't intuitive to color in. Smith Micro listened to the Manga Studio fans though, and MS5 and EX5 are now built so that it's a cinch to do all your penciling, inking, and coloring in one program.
In my time as an artist on the Internet, I can't count the number of times that I've seen a character design sheet that had a bunch of dots on it to show the base colors of a character. There's nothing wrong with putting base colors on a character reference sheet, of course, but only so long as you do it correctly. Can you remember what each color goes to? Is that blue for the eyes, or for the detailing on the shirt? Are the base color references on a separate layer so they aren't in the way of your good, finished art, or have you put them on the color layers or the ink layer and now you have...