Preheat oven to 400F.
Place a medium pan over medium heat and add ½ tablespoon oil. Add sausage and brown, 3 to 4 minutes, breaking up until mixture looks crumbled.
Transfer sausage to a plate, using a slotted spoon, and clean out excess grease from pan.
Return pan to medium heat and add remaining oil. Stir in onions and garlic and sauté for 4 to 5 minutes or until slightly translucent.
Return sausage to pan along with basil and oregano. Stir together until mixture is evenly combined.
Add marinara sauce, lower heat to medium-low and simmer for 4 to 5 minutes.
Remove from heat and allow mixture to cool, about 30 minutes.
Once mixture has cooled, fold in shredded mozzarella.
Slice each zucchini lengthwise. Using a spoon, carefully scoop flesh from each zucchini half.
Place each zucchini half, cut side up, onto a greased baking sheet.
Stuff each hollowed zucchini with sausage mixture and top with half the grated Parmesan.
Bake zucchini boats for 20 to 22 minutes or until zucchinis have softened and cheese has melted.
Remove boats from oven and cool, about 5 minutes. Top with basil leaves, red pepper flakes and serve.
