In a large braiser, or deep dish oven-safe pan, sauté the olive and onions; add in the zucchini and squash. Salt and pepper to taste.
Meanwhile, bring a large pot of salted water (I use 1/4 cup salt when using DeLallo Organic Pasta) to a boil over high heat. Add the pasta and cook for about 11 minutes. Drain in a colander.
In the “one pot,” add the drained pasta in with the vegetables mixture; add the marinara sauce and the Parmesan cheese. Gently mix, until all the pasta is coated with the sauce and the ingredients are combined. One more time, taste, and add salt and pepper as needed.
Leave the mixture in the “one pot”. Top with the fresh mozzarella slices. Bake until heated through and the top is golden and cheese melts, about 20 minutes.