In a large bowl, combine ground beef, grated Parmesan cheese, breadcrumbs, egg, minced garlic, dried Italian seasoning, salt, and black pepper. Mix until just combined.
Form the mixture into 1-inch meatballs and set aside.
Heat olive oil in a large deep skillet or Dutch oven over medium heat.
Add the meatballs in batches and cook for 4-5 minutes, turning occasionally, until browned on all sides but not cooked through. Remove meatballs and set aside.
In the same pot, add chopped onion and cook for 2-3 minutes until softened.
Add marinara sauce, water, uncooked penne pasta, and crushed red pepper flakes to the pot. Stir to combine.
Carefully place the browned meatballs back into the pot, submerging them in the sauce.
Bring the mixture to a boil, then reduce heat to medium-low, cover, and simmer for 15-18 minutes, stirring occasionally, until the pasta is tender and meatballs are cooked through.
Remove from heat and stir in chopped fresh basil and parsley.
Serve hot, topped with additional grated Parmesan cheese.