Heat the oil in a large Dutch oven over medium heat until shimmering. Add the onions & cook until golden, 10-15 minutes. Stir in the garlic, oregano and pepper flakes, and cook about 30 seconds. Transfer half of onion mixture to a bowl and set aside.
For the Marinara:.
Add the tomato paste to the remaining onion mixture in the Dutch oven and cook until fragrant, about 1 minute. Add the wine and cook until thickened slightly, about 2 minutes. Stir in the water and tomatoes and simmer over low heat until the sauce is no longer watery, 45-60 minutes. Sir in the cheese and basil and season to taste with the salt and sugar.
For the Meatballs:.
Meanwhile, adjust an oven rack to the upper middle position and heat the oven to 475 degrees. Mash the bread and milk in the bowl with the reserved onion mixture until smooth. Add the sausage, Parmesan, parsley, eggs, garlic, and salt and mash to combine. Add the beef and knead with your hands until well combined. For the mixture into 2 1/2 inch meatballs (about 16 for the full recipe). Place on a rimmed baking sheet and bake until well browned, about 20 minutes. Transfer the meatballs to the pot with the sauce and simmer for 15 minutes.