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1
Fill a large pot with lightly salted water and bring to a rolling boil over high heat.
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2
Once the water is boiling, stir in the macaroni, and return to a boil.
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3
Cook the pasta uncovered, stirring occasionally, until the pasta has cooked through, but is still firm to the bite, about 8 minutes.
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4
Drain well in a colander set in the sink.
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5
Preheat oven to 350 degrees F (175 degrees C).
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6
Spray a 9x13 inch baking dish with cooking spray, and place the macaroni into the bottom of the dish.
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7
Heat milk in a saucepan until hot but not boiling.
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8
Melt butter in a saucepan, and cook and stir the onion, garlic, and chipotle chiles until the onions are translucent, about 5 minutes.
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9
Whisk in flour, 1 tablespoon at a time, and let cook for about 3 minutes, whisking constantly to avoid burning.
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10
Whisk in the hot milk, 1/2 cup at a time, and stir in paprika, salt, and pepper.
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11
Bring the mixture to a simmer (do not boil), whisking constantly until thickened, about 2 minutes.
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12
Whisk in the cheeses, about 1/2 cup at a time, and stir until the cheeses have melted and the sauce is thick and smooth.
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13
Pour the sauce over the macaroni in the baking dish, and stir gently to combine.
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14
Cover the dish with foil.
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15
Bake covered until the dish is bubbling and the macaroni has absorbed some of the sauce, about 40 minutes.
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16
Uncover, and bake until golden brown on the edges, 10 to 15 more minutes.
