In a medium bowl, stir together the 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 to coat the base.
In a separate bowl, toss the uncooked whole grain ziti (or penne) with the remaining marinara until the pasta is well coated.
Layer the coated pasta in the slow cooker, then add a layer of sliced zucchini, followed by a layer of the cheese mixture. Repeat layers (pasta, zucchini, cheese) until all ingredients are used, finishing with the cheese mixture on top.
Cover and cook on low for 2 hours, or until the pasta is tender (al dente) and heated through.
Scoop portions onto plates and sprinkle each serving with grated parmesan before serving.