This is specific to Iodophor, but the manufacturer states that you do not have to fill a carboy up to sanitize with it. As long as you slosh enough around to get all the surfaces wet, then the sanitizer will work. Star San would work the same way, just make sure the foam touches all parts of the carboy. No need to waste sanitizer and water by making more than a gallon of solution, if you are just cleaning that one carboy.
Edit: Also, specifically for Iodophor, we home brewers typically make the solution WAY TOO STRONG. If you mix it to the proper concentration, the solution will appear like normal water with just a tinge of color. If its as dark as, say, tea, then you are making your solution too strong.