In just considering two types of Chicago Style pizzas, (1) deep dish (not stuffed) and (2) Chicago's famous thin crust styles (e.g. Vito and Nick's, Home Run Inn, Aurelio's, Marie's, etc.), the general rule IMO is that the cheese is placed first on the pizza crust on deep dish pizzas before the sauce, and with thin crust pizzas, it is the opposite with the sauce put on first and then the cheese with other toppings sometimes put under or over the cheese. This has been the "general rule" that I've found to be the case all over the U.S., not just in Chicago BTW. But, it's OK to vary that if the result is to one's liking. That's no problem, just experiment and see what you like. Either way can work very well.
If you get a soggy crust, which I rarely do with either style, there are things you can do to counter that. Like pre-baking the crust or pre-baking the crust with a little oil basted over the crust, etc., etc. A soggy crust usually results from something else, however, like too low of an oven temperature, not placing the pizza on the proper (lowest) rack in the oven, the quality of the pizza formulation (recipe) that you're using, too watery a sauce or type of cheese (I found this to be a common source of a "soggy" problem), not using the proper pan, stone, screen, or whatnot, etc, etc. It's usually not if the cheese or sauce comes on first, however. If you bake your pizza on a high home oven rack, chances are your cheese will burn long before the crust is adequately baked. Most start baking their home made pizzas on the lowest rack (or next lowest if heating elements are seen) and then put up on a higher rack at the end of the cooking cycle to brown the cheese a bit. Only practice will determine what's best for you.
I don't know if this gets at what you were talking about. If not, please reply and let us know.