Preheat your oven to 375°F (190°C).
In a mixing bowl, combine the cottage cheese with half of the shredded mozzarella and half of the grated Parmesan cheese. Mix well.
Spread the marinara sauce evenly on the bottom of a baking dish or oven-safe bowl.
Spoon the cottage cheese mixture on top of the marinara sauce, spreading it out evenly.
Sprinkle the remaining shredded mozzarella and grated Parmesan cheese over the cottage cheese mixture.
Add the diced bell peppers, sliced black olives, sliced mushrooms, and any other desired toppings on top of the cheese.
If using, add the sliced pepperoni or cooked sausage on top of the vegetables.
Sprinkle dried oregano and dried basil over the toppings. Season with salt and pepper to taste.
Place the baking dish or bowl in the preheated oven and bake for 20-25 minutes, or until the cheese is melted and bubbly, and the edges are golden brown.
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