Preheat oven to 375ºF; line a large baking sheet with foil. Bring a large pot of salted water to a boil. Cook macaroni until al dente, about 8 minutes, or as label directs. Drain; rinse under cold water.
Melt butter in a large skillet over medium-low heat. Add onion and jalapeños and sauté until soft, about 10 minutes. Sprinkle flour on onion mixture and cook, stirring constantly, 3 minutes. Slowly whisk in milk. Raise heat to medium and slowly bring to a simmer, stirring constantly. Cook for 2 minutes. Stir in chiles. Set aside 1/2 cup of Cheddar. Add remaining Cheddar and all pepper Jack to skillet and cook, stirring, until all cheese has melted. Season with salt and pepper.
Add pasta to skillet; stir. Mist a 13-by-9-inch baking dish with cooking spray and pour in pasta mixture.
In a bowl, combine corn chips with reserved 1/2 cup Cheddar; sprinkle over pasta. Place dish on lined baking sheet; bake until pasta mixture is bubbling and top is golden, 40 to 45 minutes. Let rest for 5 minutes; serve.