Preheat oven to 400°F.
Heat the olive oil in a heavy, oven-safe skillet over medium low heat. Add the thinly sliced bell peppers and onions with a hearty pinch of salt and stir to evenly coat. Cook the onions and peppers gently for 6 to 8 minutes, or until the onions are semi-translucent and the peppers are starting to soften. Add the garlic cloves, crushed red pepper, chili powder, and paprika and stir, cooking until fragrant, about 1 minute. Add the jalapeno peppers, diced tomatoes, and the juice from the whole tomatoes. Use your hands to crush and pull apart the whole tomatoes over the pan, one at a time. Stir well. Add in the stems of fresh basil and oregano, press them into the sauce with a spoon, and bring the sauce to a simmer over medium heat. Allow the sauce to gently simmer for 20 to 30 minutes, or until it has thickened and the vegetables are all very soft. Taste test the sauce and adjust with kosher salt and black pepper as needed.
*If you do not have an oven safe skillet, this is the time to transfer the sauce to a 9-inch by 13-inch baking dish or individual baking dishes.
Use the back of a wooden spoon to make 6 indentations in your sauce. Into each indentation, dollop 2 tablespoons of ricotta cheese, pressing those into the indentation, too. On top of each ricotta nest, crack one egg. Sprinkle the cheddar and Parmesan cheeses evenly over the top and pop the pan into the preheated oven. Bake for 15 to 20 minutes, or until the sauce is very bubbly, the egg whites are set and yolks are cooked to your desired doneness (See Cook's Notes), and the cheese is melted and browned around the edges. Remove the pan from the oven and garnish with additional fresh basil and oregano leaves. Serve family style in the pan with a platter of fresh toast, a bowl of olives, fresh radishes, and some fruit.