Bring a large pot of water to a boil. (Go easy on the salt; clams are quite salty.)
Heat a large (not nonstick) frying pan over medium heat and swirl in 2 tbsp. oil. Add 2 tbsp. onion and the parsley sprigs. Add as many littlenecks as will fit in one layer, then pour in 1/2 cup wine.
Crank up heat to high, cover pan, and let clams steam until they open, 2 to 3 minutes; transfer to a bowl as they open. Add remaining littlenecks to pan and cook the same way.
Strain cooking liquid through a fine-mesh strainer or cheesecloth; set aside. Once clams are cool, pluck from shells and roughly chop. Set aside in a small bowl with just enough cooking liquid to cover.
Rinse pan, then set over medium heat. Add 1 tbsp. oil, remaining onion, and a pinch of salt. Cook until tender, stirring occasionally, about 20 minutes. It's okay if onion picks up color, but don't let it burn; add a splash of water if you need to. Add chile and garlic; cook 1 minute.
Boil orecchiette until tender to the bite, 7 to 10 minutes if fresh, 15 to 20 if dried.
Meanwhile, add Manilas to onion and crank up heat to high. Add a healthy splash of clam cooking liquid or wine and cover pan. As soon as clams open, add littlenecks. Let reduce 2 to 3 minutes and add lemon juice and/or more wine to taste.
Scoop out pasta and stir into clams. Taste and adjust for salt, spiciness, and acid. Pasta should be quite juicy--if not, add more spoonfuls of clam cooking liquid, wine, or pasta water. Toss in butter and cheese and allow to melt, coating pasta. Sprinkle with chopped parsley and spoon into bowls.
*Because store-bought pasta is thinner than homemade, you get more pieces per pound.