Preheat oven to 450º. Start with cooking the pasta according to the package, al dente (be sure to salt the water). While the pasta is cooking, add butter to a large over safe skillet or dutch oven.
While the butter is melting, add chopped onions, one of the chopped jalapeños, sprinkle flour and seasonings and whisk everything together for about 2 minutes, or until the butter is melted and lightly browned.
Pour the measured milk into the mixture, turn the heat to medium low. You may need some more milk to thin and keep the cheese silky, so please keep the milk handy! Add the cheese right after the milk, mix in well, until the cheese is fully melted and the mixture is silky smooth (you can add 1/4 cup of milk more if needed!)
Add the cooked pasta to the cheese sauce, combine everything well. You can either serve as is or; what I like to do is bake it! Add 1/4 cup of (additional) cheddar over the pasta mix, add additional jalapeños for garnish. Bake in the oven on 450º for about 8-10 minutes or until everything is bubbly and lightly browned and serve.