Cook manicotti in large pot of boiling salted water until al dente. Transfer the shells to a plate to cool.
In a large sauce pan, heat the oil. Add the onions and sauté until translucent, about 5 minutes. Add the garlic and sauté for 1 minute. Add the red wine, tomatoes, red pepper and basil and simmer for 10 minutes. Remove from heat and set aside.
In a medium size mixing bowl, combine the ricotta, mozzarella and parmesan cheeses. Stir in the sausage and season to taste with pepper.
Spread about ¼ cup of sauce along the bottom of an oiled 13x9x2-inch glass or ceramic baking dish. Using a spoon, fill each pasta shell with about 1/3 cup cheese-sausage mixture. Arrange the stuffed manicotti in a single layer in the prepared dish and cover with the remaining sauce. Bake uncovered until heated through and bubbling, about 20 minutes. Let stand 10 minutes before serving.
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