In a medium bowl, stir together the fat-free cottage cheese, shredded mozzarella, kosher salt, and black pepper until evenly combined.
Pour 1 cup of the marinara sauce into the bottom of the slow cooker and spread it into an even layer.
Put the uncooked whole grain ziti shells into a large bowl and pour the remaining marinara sauce over them; toss until the pasta is evenly coated.
Layer the dish in the slow cooker: place half of the pasta-and-marinara mixture in an even layer over the sauce, top with half of the zucchini slices, then spread half of the cheese mixture over the zucchini. Repeat with the remaining pasta mixture, remaining zucchini, and finish by spreading the remaining cheese mixture on top (the cheese mixture should be the top layer).
Cover and cook on low for 2 hours, or until the pasta is al dente.
Remove the slow cooker lid and sprinkle the finely grated Parmesan cheese evenly over the top. Serve.