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1. Heat oil in a large heavy pot (big enough to hold all that sauce!) over medium heat. Cook onion and garlic until soft and translucent, about 5 minutes. Keep the lid on to help add moisture and prevent burning. Gently mix around every couple minutes to help evenly distribute heat. Add tomatoes, 1 teaspoon salt, and your desired amount of pepper. Simmer, covered, until thick, 25 minutes.
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2. Now, while that's cooking bread and fry the eggplant! Combine breadcrumbs, Pecorino Romano/Parmesan, 1/2 teaspoon salt, and some pepper. Put flour, eggs, and breadcrumb mixture in 3 separate dishes. I recommend sitting down and organizing your dishes neatly for efficient coating. Dredge eggplant in flour, shaking off excess. Dip in egg, letting excess drip off. Dredge in breadcrumbs to coat. I like to place the eggplant in the baking dish, but you can also place it in a large bowl. Dredge all of the eggplant.
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3. Heat a tablespoon of oil in a large frying pan over medium-high heat. (Oil is ready when a breadcrumb sizzles when dropped in, make sure it's piping hot!) Working in batches, fry eggplant until golden, about 2 minutes per side. Transfer to a paper-towel-lined baking sheet. Add another tablespoon of oil and repeat step. Start with the eggplant that you first dredged with, because the ingredients will have fully absorbed.
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4. Assemble the dish: Preheat oven to 375 degrees. Spread 1/1/2 cups marinara sauce in the bottom of a 9-by-13-inch baking dish. Arrange a layer of eggplant on top, overlapping slightly. Top with 11/2-cup sauce. Sprinkle with 1 cup mozzarella and 1/4 cup Pecorino Romano/Parmesan. Repeat layers one more time. Add extra cheese on the top if you like that warm gooey layer. Cover with foil and bake until bubbling, around 30 minutes. Uncover, and bake until cheese melts, about 5 minutes more.
