In a large pot or pan add a drizzle of olive oil over medium heat. Add in onion and fry until it begins to soften & brown, then add in garlic and fry for 1-2mins longer. Pour in tomato passata and add basil, chilli flakes, sugar and salt & pepper. Give a good stir then reduce to a simmer for 20-25mins until it begins to thicken. This is also important to marry the flavours together.
Pop the pasta shells in salted boiling water and cook until al dente. Knock a couple of mins off of the packet instructions, you want them soft enough to handle, but not completely cooked through or they'll come out sloppy once baked. Drain and place to one side.
Meanwhile, in a medium sized mixing bowl add ricotta, mascarpone, mozzarella, 1 cup/80g parmesan (save the rest to top) and a good pinch of salt and pepper. Stir through beaten egg until smooth and evenly combined. Place cheese mixture in a piping bag or zip lock bag with the corner cut off.
Once the pasta shells are cool enough to handle, one by one squeeze the cheese mixture into the shells. Pour tomato basil sauce into a 9x13" baking dish, then add the stuffed shells to the sauce.
Sprinkle the shells with parmesan, then crumble over crushed pine nuts. Give the whole thing a light covering of oil spray then pop in the oven at 180C/356F for 20-30mins, or until the cheese is golden and crispy.