Heat 2 teaspoons oil in a saucepan over medium heat. Add onion and 2/3 of the garlic; cook and stir until tender, 3 to 5 minutes. Mix in crushed tomatoes, tomato paste, wine, sugar, pepper flakes, oregano, salt, and bay leaf. Bring to a simmer and cook, uncovered and stirring occasionally, for 1 hour.

When the sauce has about 20 minutes left, bring a large pot of lightly salted water to a boil. Cook spaghetti in the boiling water, stirring occasionally, until tender yet firm to the bite, about 12 minutes.

While the pasta is cooking, place a steamer insert into a saucepan and fill with water to just below the bottom of the steamer. Bring water to a boil. Add clams, cover, and steam until shells open, 5 to 7 minutes. Discard any clams that do not open. Stir opened clams into the sauce.

Heat remaining 2 teaspoons oil in a large skillet over medium heat. Add shrimp and scallops; cook and stir until opaque, about 2 minutes. Stir in remaining garlic. Transfer mixture to the sauce.

Drain spaghetti. Serve seafood sauce over top and garnish with Parmesan cheese.