Both Yellow American Cheese and White American Cheese have the same fat and calorie content. The only reason Yellow American Cheese is yellow is because there is an added food coloring called annatto, that gives the yellow cheese it's distinctive flavor.
It depends on the specific cheese. The term yellow American cheese and white cheese cover many different kinds of cheeses. As a general rule, cheese that is less processed, lower in calories, fats and sodium is better. If you state the brand of each cheese, I would gladly tell you which is better.