Prep the oven and pan: Preheat your oven to 400°F (200°C). Lightly grease a large baking dish with olive oil or line with parchment.
Prepare the zucchini: Trim the ends and slice each zucchini lengthwise.
Use a spoon to scoop out the centers, leaving a 1/4-inch border to create “boats.” Chop about half of the scooped flesh and set aside; discard the rest or save for another use.
Season the boats: Place the zucchini halves cut side up in the baking dish. Brush with 1 tablespoon olive oil and season with salt and pepper. Par-bake for 8–10 minutes to soften slightly.
Sauté aromatics: While the boats bake, heat the remaining 1 tablespoon olive oil in a skillet over medium heat.
Add onion and cook 2–3 minutes. Stir in garlic and the chopped zucchini flesh and cook another 2–3 minutes until tender. Season lightly with salt and pepper.
Make the filling: In a large bowl, combine shredded chicken, sautéed mixture, cream cheese, 1/2 cup mozzarella, 1/4 cup cheddar, Parmesan, Italian seasoning, smoked paprika, and red pepper flakes.
Add marinara if using. Mix until creamy and well combined. Taste and adjust salt and pepper.
Stuff the boats: Spoon the filling evenly into each par-baked zucchini.
Pack it in so it mounds slightly.
Top with cheese: Sprinkle the remaining mozzarella and cheddar over the stuffed boats.
Bake: Return to the oven for 12–15 minutes, until the zucchini is tender and the cheese is melted and bubbly. For a golden top, broil 1–2 minutes at the end, watching closely.
Finish and serve: Let rest 3–5 minutes. Garnish with chopped parsley or basil.
Serve hot.