Preheat your oven to 400°F (200°C). Lightly grease a 9x13 inch baking dish with olive oil or cooking spray.
Prepare the zucchini boats by cutting each zucchini in half lengthwise. Using a spoon, scoop out the flesh, leaving about 1/4 inch of zucchini around the sides and bottom to create a stable "boat." Roughly chop the scooped-out flesh and set aside.
Arrange the hollowed zucchini halves in the prepared baking dish, cut side up. Brush them with 1 tablespoon of olive oil and season with salt and pepper. Bake for 10 minutes to pre-cook them slightly.
Meanwhile, make the filling. Heat the remaining tablespoon of olive oil in a large skillet over medium heat. Add the sausage, breaking it up with a wooden spoon as it cooks until it's no longer pink, about 5-7 minutes.
Add the onion, bell pepper, and reserved chopped zucchini flesh to the skillet. Cook for another 3-4 minutes until the vegetables begin to soften.
Stir in the garlic, Italian seasoning, and red pepper flakes (if using). Cook for another 30 seconds until fragrant. Remove from heat.
In a mixing bowl, combine the ricotta, half the mozzarella, half the Parmesan, and the fresh basil. Season with salt and pepper to taste. This is your cheese mixture.
Add half the marinara sauce to the sausage mixture and stir to combine. Then fold in the cheese mixture. The filling should be thick and well-combined.
Remove the par-baked zucchini from the oven. Spoon the remaining marinara sauce into the bottom of the baking dish around the zucchini boats.
Fill each zucchini boat generously with the sausage and cheese mixture. It's okay if it heaps up a bit—more is more here.
Sprinkle the tops with the remaining mozzarella, Parmesan, and the breadcrumbs for a crispy finish.
Bake for 20-25 minutes until the zucchini is tender (but not mushy) and the top is golden brown and bubbly.
Let rest for 5 minutes before serving. Garnish with additional fresh basil if desired.