In a large saucepan set over medium-low heat, melt butter and add onion. Cook for 4-6 minutes until onion is translucent and tender. Add flour and stir to combine. Lower heat to low and cook another 10 minutes, stirring occasionally.

Make bechamel: Add nutmeg and 4 cups milk and cook over medium low heat for 20-25 minutes, stirring occasionally to break up the roux until it thickens to the consistency of pudding. Add more milk if the mixture is too thick (if the spoon can stand straight up in the center of the pot). Remove from heat.

Meanwhile, preheat oven to 350 degrees F.

While the bechamel is cooking, cook the pasta al dente in boiling water according to package directions.

When bechamel is cool, fold in the cheeses, then transfer cheese mixture to a large stock pot set over medium heat. Add heavy cream and cook cheese until melted, stirring occasionally. Add cooked pasta and toss to coat it completely with the cheese. Season with salt and pepper to taste.

Transfer mixture to a large oven-safe casserole dish and bake for 20-25 minutes or until cheese is bubbly and the top is browned.