I cook ahead other than the very top layer of shredded Italian cheese which I add on the final cook to get that gooey topping. I think flavors more developed in second bake.
I use uncooked pasta when layering. My roommate from bachelor pad days always had me add “bonus” pepperoni in each layer. If you want healthy, we will also include raw spinach in the layering process. That does create liquid but you feel less guilty eating all those carbs and fats.