Preheat the oven to 450 F degrees and line a baking sheet with parchment paper.
Scoop the inside of the 6 zucchini halves using a spoon in order to make the zucchini boats.
Small dice the inside flesh of the zucchini that was removed; set aside.
Drizzle half the olive oil and salt and pepper to taste on the zucchini boats, cut side up and bake at 450 F for about 15 minutes.
While that's baking, make the quinoa stuffing. Start by heating olive oil in a medium size pan, and then cooking the onion until translucent. Add the garlic, peppers, tomatoes, chopped zucchini and crushed red pepper, and season with salt to taste.
Cook for 4-5 minutes until all the flavors are incorporated. Add cooked quinoa stir everything together for 2-3 minutes.
When the zucchini boats come out of the oven, fill them with the quinoa mixture, top with the marinara and goat cheese and bake at 450 F for about 10 minutes until the cheese is melted
Garnish with the fresh basil and serve immediately.