Preheat oven to 375 degrees F (190 degrees C). Grease a 9x13-inch baking pan with 1 tablespoon olive oil.
Heat 1 tablespoon oil in a large skillet over medium heat. Cook beef, breaking apart into small pieces using a wooden spoon, until browned, about 5 minutes. Move to a bowl using a slotted spoon.
Wipe the skillet clean with a paper towel. Heat the remaining 1 tablespoon oil. Add garlic and cook until fragrant, about 30 seconds. Add to the beef. Season beef with 1 teaspoon Italian seasoning, salt, and pepper. Stir in 1 1/2 cups marinara sauce until well combined.
Cook and stir eggplant in the skillet until soft, about 2 minutes per side. Season with salt. Set on a plate. Repeat with zucchini. Cook and stir mushrooms over medium heat until soft, about 5 minutes. Transfer to a bowl. Cook and stir Cubanelle peppers until tender, about 3 minutes.
Lay sweet potatoes evenly over the bottom of the baking pan, reserving a few slices. Layer eggplant, beef, zucchini, Cubanelle peppers, and mushrooms on top. Cover with the remaining 1/2 cup marinara. Top with the reserved sweet potato slices. Drizzle with oil; season with the remaining 1 teaspoon Italian seasoning, salt, and pepper. Cover with aluminum foil.
Bake in the preheated oven until sweet potatoes are soft, about 45 minutes. Remove aluminum foil and bake until golden brown, about 15 minutes more. Let rest for 5 minutes before serving.
