Stir ground beef, sausage, basil, oregano, pepper, and salt together in a bowl.
Cook and stir beef mixture in a large skillet over medium-high heat until browned and crumbly, 7 to 10 minutes.
Heat olive oil in a skillet over medium-high heat. Saute onions and garlic in hot oil until slightly golden and tender, 10 to 12 minutes.
Stir beef mixture, onion mixture, tomato sauce, crushed tomatoes, diced tomatoes, and red peppers together in a large bowl.
Stir 1 cup mozzarella cheese, ricotta cheese, and Parmesan cheese together in a separate bowl.
Spoon 1/3 of meat mixture into the slow cooker; top with 1/2 the ziti pasta. Drop 1/2 the cheese mixture by rounded tablespoons over the ziti; carefully spread cheese mixture over ziti using the back of the spoon. Repeat layering process 1 more time. Pour remaining meat sauce over the top and place the lid on the slow cooker.
Cook on Low for until ziti is tender, 6 to 7 hours (or cook on High for 3 to 5 hours).
Sprinkle remaining 1 cup mozzarella over the top of the baked ziti and let stand until melted, about 10 minutes.