Preheat the oven to 350 degrees.
Generously spray 8 cups of your muffin pan with cooking spray.
In a large bowl, combine the crushed Ritz crackers, 1 cup of the shredded cheddar cheese, and the melted butter, mixing well until the mixture holds together and resembles coarse sand. Divide the mixture among the 8 muffin cups and, using your fingers, press the crust firmly into the bottoms and up the sides of each muffin cup.
In another large bowl, combine the cooked (and still hot) macaroni with 1/2 cup of the shredded cheddar, the garlic & herb cheese, and the butter. Mix well.
In a separate small bowl, combine the eggs, milk, sour cream, salt, and red pepper flakes (if using) and mix well. Add the egg/milk mixture to the cooked macaroni, mixing until all of the ingredients are melted and smoothly combined. Place about 2-3 tablespoons of the macaroni mixture into each muffin cup.
Top each muffin cup with the remaining cheddar cheese. Bake the mac and cheese cups until lightly golden on top, about 20-25 minutes. Let cool slightly before removing from the muffin pan. Use a fork to gently remove from the muffin pan.