Preheat oven to 400 degrees F. Line a baking dish with parchment paper and set aside.
Cut each eggplant in half lengthwise. Score the eggplant and scoop out the flesh, creating a little boat of the shell. Rub the inside of the hollow eggplant boat with a drizzle of olive oil and a sprinkle of salt and pepper. Place the shells in the baking dish, cut-side up and roast until tender, about 20-30 minutes.
Chop the flesh of the eggplant coarsely and set aside. In a bowl, combine breadcrumbs, 1 tsp olive oil, and a pinch of salt and set aside.
Heat 2-3 tbsp olive oil in a large skillet over medium heat. Add onions and cook until softened, about 4 minutes. Add garlic, chopped eggplant, and a sprinkle of salt and pepper. Cook until eggplant is tender, about 8 minutes. Stir in 2 cups of marinara sauce and cook for another 2-3 minutes, then add basil and mix.
To the baking dish, add 1 cup marinara to the bottom. Place cooked eggplant shells on top of the marinara sauce. In each eggplant shell, add 1 piece of sliced mozzarella, then scoop in about 2 spoonfuls of the filling. Top with another slice of mozzarella, a sprinkle of parmesan cheese, and some of the breadcrumb mixture. Repeat until all eggplants are done.
Place in broiler on HIGH until cheese is melted, bubbling, and brown, about 2-4 minutes. Watch closely. Sprinkle with more basil and enjoy!