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As you can see, you can specify the color of various parts of the home and away uniform. Each of those buttons is a "color picker" that lets you choose any color in the spectrum. You can even assign pinstripe colors (or choose no pinstripes).
Each team has 4 alternate uniforms, and the option to choose which days of the week (if any) they are used. Mogul currently loads the 2013 uniforms (and any official alternate uniforms) automatically. A database of uniforms for the last 110 years will be included with the final version.
These uniforms are used for all the batter and pitcher animations, and combined with the correct skin color for the player in question.