In a large saute pan over medium heat, add 1 tablespoon oil and saute onions, bell peppers and garlic. After 2 minutes, add salt and cook until tender. Remove from pan and let cool.
In a medium bowl, pour milk over bread crumbs and let soak for 5 minutes. Remove from milk and squeeze out excess milk, until bread is moist but not soggy. In a large bowl, mix together beef, pork sausage, soaked bread, cooled vegetables, basil, oregano, parsley, pepper, chili flakes, grated Parmesan and egg. Gently roll into 2-inch balls.
In same large saute pan used for vegetables, heat over medium heat and add 1 tablespoon oil. Cook meatballs, browning completely until the internal temperature reaches 165 degrees F, using an instant-read thermometer.
Meanwhile, remove inside dough from hoagie rolls. To assemble heroes, fill hoagies with 4 meatballs each. Drizzle with 1/4 cup Marinara Sauce and top with 3 slices of mozzarella cheese. Place heroes on a sheet pan under the broiler until the cheese melts and turns golden brown. Top each sandwich with 1/2 tablespoon Parmesan.
In medium saucepan, heat olive oil, add onions and cook over medium to low heat until onions are transparent. Add garlic and cook until almost brown and then add tomatoes. Cook for 1/2 hour over low to medium heat, then add basil and oregano and continue to cook for 30 minutes longer. In a food mill or a blender, puree into a sauce. Season with salt and pepper, to taste.