Preheat oven to 350°. Spread 1 cup of marinara over the bottom of a 9x13-inch baking dish. Using a spoon, hollow out eggplants, leaving about a 1/2-inch-thick border around skin to create a boat; transfer to baking dish. Roughly chop scooped-out eggplant flesh.
In a large skillet over medium heat, heat oil. Add onion and cook until soft, 5 minutes. Stir in chopped eggplant and season with oregano, salt, and pepper. Cook, stirring often, until golden and tender, 3 to 4 minutes. Add garlic and cook until fragrant, 1 minute.
Transfer mixture to a bowl and add tomatoes, egg, 1 cups of mozzarella, and remaining 1/2 cup marinara. Mix until just combined, then scoop into eggplant boats. Top with remaining 1 cup mozzarella, Parmesan, and bread crumbs.
Bake until eggplants are tender and cheese is golden, about 50 minutes.
Garnish with basil before serving.
