Preheat the oven to 375 degrees F (190 degrees C). Lightly grease a mini muffin pan.

Bring a large pot of water to a boil over high heat.

Heat a large deep skillet over medium-high heat. Add ground beef and cook, crumbling with a spoon, until browned, 5 to 7 minutes; drain any excess grease. Add onion and cook until softened, 3 to 4 minutes. Stir in marinara, 1 teaspoon salt, pepper, garlic powder, and Italian seasoning. Bring to a simmer, reduce heat, and cook for 20 minutes, stirring often.

Add remaining 3 teaspoons salt and pasta to boiling water and cook, stirring occasionally, until tender, 10 to 12 minutes. Drain, rinse with cold water, and drain well.

Turn pasta shells inside out and place 24 shells into the prepared muffin pan. Save any broken or remaining shells for another use.

Fill each shell with about 2 teaspoons ricotta and sprinkle 1/4 cup Parmesan cheese evenly over the ricotta. Top with about 1 tablespoon meat sauce and top evenly with mozzarella and remaining Parmesan.