While the squash roasts, heat the reserved oil in a large skillet over medium heat; add the italian sausage and cook, breaking it up, until browned, 5–7 minutes, then stir in the yellow onion and cook until translucent, 4–5 minutes; add the garlic, crushed red pepper flakes, and dried oregano and cook until fragrant, about 1 minute; stir in the marinara sauce and simmer gently to thicken slightly, 5 minutes.
When the squash is cool enough to handle, turn the halves cut side up and use a fork to scrape the strands into the skillet, leaving the shells intact; toss until the strands are well coated with the sauce.
Spoon the mixture back into the shells, mounding it evenly; top with the mozzarella cheese, then the parmesan cheese.
Return the stuffed shells to the oven and bake until the cheese is melted and bubbling, 10–12 minutes; for deeper browning, broil 1–2 minutes, watching closely.
Let rest 5 minutes, finish with the fresh basil, and serve hot.