Making a perfect, gooey, cheesy, filled omelette can be tough to time just right without overcooking the eggs, but Serious Eats has a tip that will help: mix your cheese with your fillings first, then fill the omelettes second. Here's how it works.
Image from J. Kenji López-Alt.
Filled omelettes usually have other ingredients (like ham or veggies) that need to be cooked before being added to the eggs in the pan. Don't be tempted to try and cook your fillings along with your eggs, or you'll wind up with a scramble. Instead, cook your fillings first, then mix shredded cheese with the filling when you take them out of the pan to start cooking the eggs.
It's a simple step, but adding the warm fillings to the cheese before you add them back to the eggs will start to melt the cheese from the heat of the fillings. By the time the eggs are ready and you pour everything in and roll it up, it will be perfect. A little extra heat as the eggs finish cooking in the pan and you have a perfectly cheesy omelette.
The Food Lab: A Quick Guide to Stuffing Omelettes [Serious Eats]