Cover and cook on low for 1 to 2 hours, until the pasta is chewy (not quite crunchy, but very al dente). Your cook time will vary if you use a different pasta, so start with 1 hour and adjust from there. Stir once halfway through the cook time and be sure to smooth the pasta into one layer so it is well coated with the sauce. Once the pasta is ready, sprinkle on the cheddar and pepper Jack cheeses and stir to combine. The cheese will melt into the sauce to create the most luxurious creamy cheese sauce. Cover the mac and cheese and cook for 10 minutes, until the cheese is melted and it comes together. Stir before serving.