Preheat oven to 350°F
Cook pasta shells to al dente according to package instructions. Drain and set aside.
While the pasta cooks, heat olive oil in a large skillet over medium heat. Add onion, zucchini, squash and bell pepper to the pan.
Cook 3-4 minutes until vegetables begin to soften. Add spinach. Stir until spinach wilts. Remove pan from heat and cool slightly.
Meanwhile, in a medium bowl, combine ricotta, mozzarella, egg, Italian seasoning, and red pepper flakes. Add vegetable mixture to cheese mixture and stir until fully combined.
Spread ¾ cup of marinara sauce in the bottom of an 11X7 or 8X8 baking dish.
Carefully stuff each shell with 2-3 Tablespoons of vegetable mixture. Place stuffed shells in even rows in the baking dish. Top with remaining sauce.
Cover dish with foil and bake for 35 minutes. Uncover, sprinkle parmesan cheese evenly over the top.
Bake, uncovered, for 10 minutes more until cheese is melted and bubbly.
Remove from the oven. Let cool slightly. Serve warm!