Note: The reason you want your tomatoes seeded, and squash small, is because excess moisture will make your pie soggy.
Layer 1: Caramelized onions
Layer 2: Jarlsberg cheese
Layer 3: Zucchini
Layer 4: Mozzarella cheese
Layer 5: Egg mixture
Layer 6: Yellow Squash
Layer 7: Sliced Tomatoes
Layer 8: Parmesan cheese
Layer 9: The rest of your salt and pepper
Layer 10: Crushed oregano
Note if you start your onions in a dutch oven, you can layer right into the pot when the onions are done. Then put it straight into the oven to bake. Your baking time may vary.