While the pasta is cooking, prepare the filling. In a large bowl, mix all of the filling ingredients together. Season with salt and pepper.
PREPARE THE SAUCE:
In a medium saucepan, heat the butter over medium-low heat until melted. Whisk in the flour and stir until smooth. Over medium heat, cook until the mixture turns a golden sandy color, about 6 to 7 minutes. Meanwhile, heat the half and half and milk in a separate pan until just about to boil. Add the hot milk to the butter mixture 1 cup at a time, whisking constantly until very smooth. Bring to a boil- stir and cook for 8 to 10 minutes, then remove from heat and stir in the salt and cheese. Set aside until ready to use.
ASSEMBLE THE SHELLS:
Preheat the oven to 350℉. Spray a 9x13-inch pan with nonstick spray. Pour about 1½ cups sauce into the bottom of the pan. Fill the shells with the cheese mixture and set them in the pan (6 rows x 4 rows). Drizzle the remaining sauce on top. Sprinkle basil and chives (if using) on top, then sprinkle with salt and pepper.
Bake 30 minutes, or until the shells are hot and bubbling and heated through. Leftovers keep well (and my husband says they're even better the next day!)
Notes
I always make a few extra shells since some of them inevitably tend to break apart while boiling.
Substitute marinara sauce for the white sauce, if you'd like