If you want to make plain omelet, only fill the muffin pan with half the egg mixture or else it will rise like a souffle.
You can also break and add one egg into individual cups. Turns out like poached eggs.
Vegetables can be added without sauteing if you don't mind the rawness. I sauteed mine in 1 teaspoon of oil before adding to the cupcake pan.
If you are only making 6 omelets in a 12 cup cake pan, fill the remaining cups with 1/3 water so that everything cooks evenly and the cooking time stays the same.