Preheat the oven to 400f and set the rack to the middle level.
Bring a pot of water to boil (large enough to fit the zucchini boats).
Remove zucchini seeds with a spoon, leaving ¼-inch interior walls.
Boil the zucchini boats for 2 minutes then drain and run under cold water until cool and set aside.
Saute the onion in the olive oil over medium-low heat until soft (about 5-7 minutes) then add in the garlic and saute for another 2-3 minutes until golden.
Add in sausage, turn heat to medium, and saute for around 7 more minutes or until mostly cooked through. Use a wooden spoon to break up the sausage into small pieces.
Remove the pan from the heat. Add in the breadcrumbs, basil, ½ cup mozzarella, ½ cup Pecorino Romano, and a ½ cup of marinara sauce. Mix well.
Place a thick layer of marinara sauce into a large baking dish.
Dry off the zucchini with paper towels. Season the inside of the zucchini with salt and pepper to taste.
Stuff each zucchini boat with the stuffing and place each boat into the baking dish.
Spoon the remaining sauce over the top of each boat and sprinkle with the remaining Pecorino Romano and mozzarella cheese.
Bake the zucchini boats until fork tender (around 25 minutes) covered with foil.
Remove foil and broil for 2-3 minutes more to brown top. Watch carefully for burning.
