Preheat oven and heat frozen meatballs according to package directions.
Bring a large pot of salted water to a boil. Add about 12 oz. (about 3/4 of a package) of macaroni, penne, gemelli, or similar pasta. Cook until just tender, about 10-12 minutes.
Combine flour, cayenne, garlic powder, onion powder, salt and pepper in a small bowl.
Dice jalapeno into small pieces and place in pan with butter. Melt butter with jalapeno on medium low heat until butter is melted and jalapeno just starts to soften, about 2 minutes.
Sprinkle flour and spice mixture into the pan with butter and stir to combine into a paste. Let the flour cook, stirring often, for about 30 seconds.
Add a splash of milk, no more than 1/4 c., and stir into the flour mixture. It will look like something went wrong and the mixture has seized up. When the milk and flour are well combined, add another splash of milk and stir until combined.
Continue adding the milk in increments, increasing the amount of milk slightly each time and stirring the paste until no lumps remain. It should take about 4-5 additions to incorporate all of the milk. Your goal is something that looks like the consistency of a cream soup.
Reduce heat slightly and add the cheese. Stir occasionally until all the cheese is melted. Taste and season with salt as needed. Keep warm until ready to use.
When pasta is ready, drain it in a colander and return it to the pan. Off heat, stir in the cheese sauce and cooked meatballs.