The best way to store food in a microwave using aluminum foil is to avoid using it altogether. Aluminum foil is not recommended for use in microwaves because it can cause sparks and potentially start a fire. Instead, use microwave-safe containers made of glass, ceramic, or plastic. If you must use aluminum foil, ensure it does not touch the microwave's walls or ceiling and that it is not in direct contact with the food. However, for safety and efficiency, it's best to use appropriate microwave-safe materials.