I've been making deep dish Chicago style pies for over two decades now, one thing I never
change is the sauce. It's simple: for two pizzas I take three 28oz cans of peeled tomatoes (with or without basil added), drain them really well, break up the tomatoes and drain that. Throw in a bit of sugar and some oregano and mix it up. Let it sit for at least 30 minutes and drain once more before putting the tomatoes on the pie.
Sauce always goes on top of the cheese and ingredients, some parmesan on top of the pie and the rest is magic.
I use this recipe for 12" deep dish pies (EDIT: measured my pans, they're 14"ers, heh). Like I said, the sauce is the only thing that never changes, it doesn't have to, I've changed everything else about my pizzas over the years to get to where they're at now, and the sauce is the one part I've never felt needed to be different. I always get the perfect tangy taste of tomatoes on my pies, and they're not watery, which is amazing since I use at least a pound of mozz per pie. Sweated mushrooms and onions and bell peppers go really well with this. As does just cheese and a pound and a half of cooked italian sausage. Used two half lb Armadillo Eggs on a pie recently, been saving that for another post with pics, was inspired by Rick's Tropical Delight. But the sauce went well with that too.
Tomatoes on top of veggies, 2lbs of sweated mushrooms, 1.5 lbs of italian sausage, 1 lb of mozzarella:
Tomatoes on top of two half pound Illinois Armadillo Eggs (BBQ rubbed, 2/3 pork sausage, 1/3 ground chuck, 1 big jalapeno stuffed with cheddar) on top of 1 pound of mozzarella:
Everyone I've made these for (friends and relatives birthday parties usually) claims they're the best pizza they've ever had. They probably haven't eaten as much pizza as I have, but they're happy. :D