Preheat the oven to 375° F and line a baking sheet with parchment paper.
Roast the spaghetti squash cut side down for 45 minutes or until just tender.
Let the squash cool slightly or use an oven mitt to hold it while you scrape out the ‘pasta strands’. Lightly mix the squash with the marinara sauce and sea salt.
Spoon the filling back into the squash skins. Using the remaining 1/2 cup marinara sauce, top the squash boats with about 2 Tablespoons each. At this point, you can refrigerate until the next day.
If you’re using the squash boats right away, top with the sliced mozzarella and bake for 15-20 minutes until the cheese is bubbly. If you’re baking the boats right out of the refrigerator, top with the cheese and bake for 45 minutes or until the cheese is bubbling and the squash boats are heated through.
Serve immediately with fresh basil, and freshly ground black pepper.