Heat a large skillet over medium-high heat and stir in the Italian sausage. Cook and stir until crumbly, evenly browned, and no longer pink. Drain and discard any excess grease, then remove the sausage from the skillet and place into a bowl.
Heat 1 tablespoon of olive oil in the skillet. Stir in the onion, green bell pepper, and red bell pepper; cook and stir until the onion is golden, and the peppers are tender, about 8 minutes. Stir in the garlic and mushrooms; cook for 1 minute more. Season with parsley, garlic powder, oregano, basil, and red pepper flakes. Season to taste with salt and pepper. Stir to combine, then scrape the vegetables into the bowl with the sausage.
Heat 1 tablespoon of olive oil in a large skillet over medium-high heat. Place the pierogies into the hot oil, and cook until golden brown on each side and hot in the center, about 5 minutes. Spoon the sausage and vegetable mixture over the pierogies. Sprinkle with mozzarella cheese and Romano cheese. Cover, and cook until the cheese has melted.