Heat the oven to 400°F and line a baking sheet with parchment paper. Carefully halve the spaghetti squash lengthwise, then scoop out and discard the seeds and stringy pulp.

Brush the cut sides with olive oil and season with about 1/2 teaspoon kosher salt and 1/4 teaspoon black pepper. Place the squash cut-side down on the prepared baking sheet and roast for 35–45 minutes, until the flesh separates into strands with a fork.

While the squash roasts, heat a skillet over medium heat. Cook the ground beef or Italian sausage with the chopped onion for 5–7 minutes, breaking the meat into small pieces, until browned and the onion is soft.

Add the minced garlic and cook for about 30 seconds, just until fragrant. Drain excess fat if necessary, then stir in the marinara sauce, Italian seasoning, remaining salt, and remaining pepper; simmer for 5 minutes.

Let the roasted squash cool for several minutes so it is easier to handle. Use a fork to loosen the flesh into spaghetti-like strands, leaving those strands inside the shells.

Mix the squash strands with the meat sauce directly in the shells, or spoon the sauce over the strands for a more defined layered look. Divide the filling evenly between the four squash halves.

Sprinkle the mozzarella and Parmesan over each boat. Return the baking sheet to the oven and bake for 8–12 minutes, until the cheese is melted and hot.

For a browned cheese topping, broil the boats for 1–2 minutes while watching closely. Garnish with chopped basil or parsley and serve hot.