I'm trying my hand at making a thin crust homemade pizza and the dough turned out pretty well except that the cheese was getting overdone/burned before the bottom of the crust browned ....
My first try was not a thin crust and tried pre baking the dough for about 8 min or so and I didn't like the thickness or the chewiness from the pre baking.
My second try was with the thin crust (no pre baking) and I used a new pizza stone (not preheated) with oven temp at 450 and the cheese started to burn before bottom was browned.
My third try was thin crust, but preheated the stone and tried the oven at 425. But I still had the problem of the cheese burning before the bottome was browned.
And another detail (not sure if this mattered) - after the first rise, my recipe called for the dough to be punched down and put into large ziploc bags in the refrigerator overnight. Then the dough needed to be taken out and brought to room temp before using. I followed these directions, except my house is rather cold, so my dough was rather cold when I rolled it out.
I always prebake the crusts. I like a thin, crispy crust. Then, I put on the toppings and put the pizza back in, directly on the rack.
I have lots of pizzas on my blog, with pictures.
I had a pizza stone, but broke it early on and really didn't want to replace it. I don't do anything special, no special ingredients or tools.
First, I'm still using yeast that is 6 years past the stated expiration date. It is kept in a glass jar in the fridge. I buy yeast in 2 1-pound packages at BJs, and share 1 pound with my son-in-law. I allow the dough to ferment for about 16 hours before starting to roll out the pizza, and we like thin crust.
Suggestion: preheat pizza stone for 1/2 hour after oven reaches desired temperature. Since you are having a problem with cheese burning, top the pizza with everything but the cheese, and then place in the oven for a few minutes before adding the cheese. I don't prebake the dough because of dough bubbling problem. After the pizza has been in the oven for a while, add the cheese and watch it melt. See if that solves your problem, a problem that I never had.
I just wanted to second the preheat the stone for an extended period of time. Preheating your oven and preheating the stone are not the same thing. It will take a while at the desired temp for the stone to properly heat up. I preheat my stone for about an hour actually when doing pizzas in the oven.
My second questions would be where in your oven is the stone located? (Top rack/bottom rack/middle?) If your problem is top browning (i.e. cheese burning) then make sure the stone is at the bottom of the oven.
If that doesn't help let us know more about your dough recipe and type of cheese your are using. If you didn't like the thickness of your pre-baked crust I'm wondering if your dough has too much flour making it dense (and slow to cook and get crispy) or if you just aren't rolling/stretching your crust thin enough.
Get a copy of Cook's Illustrated thin crust pizza from Feb/Mar 2010. You bake on a preheated pizza stone at 500 on the top shelf of your oven. My oven goes to 550 and it takes 10 minues for me to bake. I have made over a 100 pies this way and won't go back to another method. The rub is that you need to make the dough in advance and refrigerate for 24 hours but the dough freezes well if you want to make it advance and defrost. Just a great guide to getting excellent pie at home.
I make a thin crust pizza every Friday night. I use a perforated pizza pan. I bake the crust with toppings at 440 deg F for 9 minutes. I take it out, put the cheeses on and bake for an additional 5 minutes; then take the pizza off the pan and place directly on the rack for 2 minutes. I've baking pizza this way for years and it turns out great everytime. I have a pizza stone but it's really just easier to bake in the pan. We like having the cheese on top of the toppings but if you like the cheese on top of the sauce with the toppings over the cheese, prebaking the crust would be the way to go. Good luck!