Preheat the oven to 375 degrees F. Line a 13x9-inch rimmed baking sheet with parchment paper.
To make the meatballs: in a large bowl, stir together the ground chicken, ½ cup bread crumbs, ¼ cup parmesan, 1 tablespoon Italian seasoning, garlic, egg, ½ teaspoon red pepper flakes, ½ teaspoon salt, and ¼ teaspoon black pepper until well combined. Scoop the meatball mixture into twenty 2 tablespoon-sized portions. Flatten each meatball and place a mozzarella ball in the center. Re-form into balls around the cheese to completely cover the cheese.
To coat the meatballs: fill a shallow bowl with the flour. In a second shallow bowl, whisk together the eggs and milk until pale in color. In a third shallow bowl, stir together the 1 cup bread crumbs, ½ cup parmesan, 1 teaspoon Italian seasoning, ½ teaspoon red pepper flakes, ¼ teaspoon salt, and pinch of black pepper until well combined.
Working with one meatball at a time, roll the meatball in the flour to lightly coat it, gently tapping off any excess. Transfer the flour-coated meatball to the egg mixture and coat on all sides so that there are no visible flour spots. Finally, generously coat the meatball in the bread-crumb mixture. Place on the prepared baking sheet. Repeat with the remaining meatballs. Spray the meatballs all over with cooking spray to help them crisp as they bake.
Bake for about 20 minutes or until golden brown and crisp. Remove from the oven. Set a rack in the middle of the oven, then turn the oven to broil.
Scoop 1 teaspoon of marinara sauce on top of each meatball, then top the sauce with a mozzarella half. Return the meatballs to the oven and broil for 2-3 minutes, until the cheese is melty and bubbling brown in spots.
Garnish the meatballs with grated parmesan and chopped basil and serve with more marinara sauce for dipping.