Do not drain the tomatoes. Use seasoned bread crumbs for more flavor.
Most home cooks ruin baked pasta dishes by rinsing the noodles under tap water after boiling, which strips away the external starches necessary for sauce adhesion. Cook the pasta one minute shy of the package instructions so the starch holds firm during the subsequent twenty minutes in the 325-degree oven. Never rinse freshly drained shells, as that missing starch layer prevents the tomato mixture from clinging properly to the surfaces.
Pouring off the liquid from canned tomatoes turns a rich bake into dry, cardboard-like layers. Retain all canning juices to provide the necessary moisture for hydrating the pasta grains as they absorb liquids during the baking cycle. When simmering the shallots and minced garlic in olive oil over medium heat for five minutes, watch for a pale golden hue rather than deep browning to avoid bitter aromatic flavors.
Layering requires precision to ensure even heat distribution through the casserole dish. Distribute one-third of the sauce, pasta, and cheeses sequentially, repeating this pattern three times before finishing with the reserved bread crumbs and grated parmesan. Visual doneness relies entirely on the surface coloration; pull the casserole from the oven when the top layer turns a distinct golden brown and the edges bubble vigorously.