Start with the sauce as it will simmer for a while — peel and dice up the onion and peel and slice the garlic lengthwise.
Pour the whole tomatoes into a bowl and crush them by hand. If you’ve never done this before just take a whole tomato in your hand and squeeze gently. Make sure to keep it down low or almost submerged because it will splash., but don’t be nervous, it’s fun! Continue to crush the tomatoes until they are a more uniform and mushy consistency.
Set a pot or dutch oven over medium heat and add extra virgin olive oil. Add the onions and a pinch of salt and sauté until translucent, stirring as needed, about 3-5 minutes.
Add the garlic and saute until fragrant, being careful not to burn, about 2 minutes.
Stir in the tomato paste and cook off for a minute or two before adding the pasta and crushed tomatoes. Rinse the tomato can with a bit of water and add that as
well.
Stir everything together and add a few pinches of kosher salt. Throw in a parmesan rind if you have one.
Lower the sauce to a simmer and cook for about 2 hours, stirring now and then so that nothing burns and it cooks evenly. Taste and adjust, adding salt little by little as necessary.
While the sauce is cooking, mix the filing for the shells. Add the ricotta, mascarpone, and pecorino to a bowl with a few small pinches of salt and whip with a whisk. This helps the aerate the cheeses a bit for a nice light bite. Taste and adjust, adding salt as necessary, and black pepper if you’d like (though I prefer mine without).
If you’d like, transfer the cheese to a piping bag to more easily fill the shells. Refrigerate the piping bag or mixing bowl of cheese until you’re ready to fill the shells.
Once your sauce is almost finished, boil the shells until al dente according to package instructions.
Remove the shells and allow them to cool off on a baking sheet until cool enough to handle.
Preheat your oven to 400 F.
When ready to assemble the dish, add a few ladles of the sauce to a casserole dish or baking dish. Fill each shell with the cheese and nestle them into the sauce, packing the shells close together. Once finished, top with an extra grating of parmesan cheese, and/or some more sauce grated mozzarella if you’d like.
Bake for about 30 minutes. Top with an extra grating of parmesan and some basil if you’d like. Enjoy!