I have the recipe for "Deep Dish" crust from Encyclopizza. After making that, how do I get a thick, deep dish crust?

you need to proof your dough at 90 degrees +/- 5 degrees from a half hour to 1.5 hours

We use a "sheeter" for our thin-crust, and bulk dough. Would we still do that?

To make a good deep-dish (thick crust) pizza, I like to use a dark colored pan 1.5 to 2-inches deep. Use shortening, margarine, butter, salad oil/vegetable oil, or olive oil in the pan. Experiment to see which one works best for you and gives the flavor characteristics that you like the most. Be a bit on the generous side when applying the fat to the pan as it will contribute towards a fried rather than baked crust characteristic. My own preference is to sheet or roll the dough out to a size that can be dropped into the pan having it completely cover the bottom. You can also form the dough to the pan by hand. In this case you might like the way a solid fat (butter, margarine, shortening) holds the dough in place while you're pressing the dough into the pan. After you have the dough in the pan, you will need to either place the panned dough in a proofer at 90 to 95F with 75 to 78% relative humidity, or, cover the pan with a pan separator or stacking lid, or use self stscking/sealing pans and set aside in a warm place to rise for 30 to 70 minutes. Adjust the time to give you the finished crust thickness and lightness that you want. A good starting point for scaling weight is about 14-ounces in a 12-inch deep-dish pan. If you will be baking these in a deck oven, you might want to try using a screen under the pan to prevent getting excessive bottom bake color. In an air impingement oven we typically need to bake these pizzas about 25F cooler and about 2 minutes or so longer than a thin crust pizza. Recent work that we've done with the new, Lincoln Fastbake oven indicates that we might be able to bake both thin and deep-dish pizzas side by side at the same time and temperature. Now that's progress.
Tom Lehmann/The Dough Doctor