Thaw the squid tubes, drain, pat dry.
Using a skillet, heat ¼ cup olive oil over medium heat.
Add the onion and cook for approximately 2 minutes, until softened.
Add the garlic and red pepper flakes. Sauté for 2 minutes.
Add chopped parsley and Parmesan cheese. Mix well and remove from heat.
Stuff each squid with the filling, leaving the bottom and top inches unfilled. Secure the tops with toothpicks and season all over with salt.
For the sauce:
Using a deep pan, warm ¼ cup olive oil over medium heat.
Add the garlic. Cook until fragrant and beginning to color.
Stir in the tomatoes, adjust salt and pepper.
Bring the tomatoes to a boil, then lower the heat and simmer the sauce for 15 minutes.
Add the stuffed squid, cover the pan and simmer for 20-35 minutes, stirring occasionally.
Garnish with parsley and serve with crusty bread.
Serve it hot.