Cut the squash in half lengthwise. Scoop out and discard the seeds.
Preheat the oven to 400 degrees. Place squash halves cut side up on a baking sheet. Brush with some vegetable oil and season with salt and pepper. Roast for about 45-50 minutes, or until a fork punctures the flesh of the squash easily. If the squash seems to be drying out while baking, brush with an additional tablespoon oil. Remove squash from the oven and allow it to cool just enough so you can handle it, about 3 to 4 minutes. Scrape the flesh from the squash into wonderful, stringy "noodles" with a sturdy fork and place in a small serving bowl. If some of the strands clump or gather together, simply separate them using your hands.
Heat the olive oil in a large skillet over medium high heat. Add onions and garlic to the skillet and sauté until onions are translucent. Add the tomatoes and sauté for another 5 minutes, or until tomatoes have begun to break down. Add the tomato paste, salt, pepper, oregano and basil and stir to combine. Reduce heat to low, cover and let sauce simmer for 15 – 20 minutes, stirring occasionally. With roughly 5 minutes left to simmer, taste the sauce and adjust the seasonings according to your preference.
Add the honey (optional). Once the sauce has broken down, turn off the heat. Using an immersion blender to blend the sauce together until smooth.
Preheat the oven to 350 degrees. Cook the quinoa according to the directions on the bag. Let cool for 10 minutes or until at room temperature. Combine cooked quinoa, tomato paste, egg, almond flour, oregano, garlic powder, salt and pepper into a mixing bowl and stir until all ingredients are equally mixed. Using wet hands, form quinoa mixture into 1-inch balls. Arrange meatballs on a rimmed baking sheet sprayed with oil, and bake about 15-20 minutes. Sprinkle the dish with grated cheese to taste.
Prep Ahead Guide: These meatballs can be done up to 4 days in advance. Rewarm in a 350 degree oven until heated through.
Freezer Instructions: Meatballs can be frozen for up to a week. Rewarm in a 350 degree oven.
Leftovers: Can be kept in an air-tight container for up to a week.