Where is the best/authentic place to layer the pepperoni?
The first answer that came to mind is "wherever you like it." Some pizzerias put it deep under the sauce, some just slightly under the sauce, and some on top of the sauce, and some do a combination of under and over the sauce. Most of my friends and relatives don't like it under the sauce too much as we prefer some degree of crispness to the pepperoni and under the sauce it generally remains wet and chewy, and much of the grease from the pepperoni melts out into the rest of the pizza. But many like it that way and that's all right.
And the problem with putting it on top of the sauce is that because of the long baking cycle of a deep dish pizza, the pepperoni would likely become burnt by the time the pizza is done. What I like to do is put the pizza in the oven without any pepperoni on it. Or if doing the combo technique putting a little bit of pepperoni under the sauce but reserving the majority of the pepperoni to add on top of the sauce late in the bake cycle. And before adding the remaining pepperoni, I "nuke" the pepperoni on paper towels in the microwave for 15 to 20 seconds, careful not to do it too long. And when the pizza has roughly 5 or 10 minutes remaining to be baked (sometimes easier said than done in determining that) I pull the pizza out and put the previously "nuked" pepperoni on the pizza (in my case most commonly on half of the pizza). And then back into the oven for 5 or 10 minutes. (If your oven has a "convection" feature, this is a good time to use it, but not before).
Here's a picture of one I did recently following this way of thinking. I may have put it into the microwave a little bit too long . . . or in the oven a little bit too long after adding it . . . BUT I got absolutely no complaints and only praises for how good every aspect of the pizza was. While the pepperoni looked slightly well done, it was well received that way. But in any event, you're in control of how you want it done. Good luck and let us know which way you've come to like it the best.