jcg,
I saw your post over at the Chicago board after I posted. However, before extrapolating from a 10" pan (which I assume is 2" in depth and straightsided) to a like pan but 12" in diameter, I'd like to first determine the thickness factors for the inside and outside skins for the 10" size. For example, the article you referenced says to use about 2/3 of the total dough weight for the inside skin and the remaining approximately 1/3 of the total dough weight for the outside skin (the very thin one). The article also says that one should roll out the inside skin to at least 14" for the 10" pan. If we use 14" as the number, that means that the inside skin covers the bottom of the pan (10") and the sides of the pans (2"). So, 10" + 2" +2" = 14". My recollection is that when Boy Hits Car (Mike) and I designed the deepdish dough calculating tool at
http://www.pizzamaking.com/dd_calculator.html, we intended that the inside skin fit the pan in the desired manner without overlapping the pan at the top.
So, the Zachary's numbers for the inside skin seem to fit the deepdish dough calculating tool as we intended. With this in mind, I used the deepdish dough calculating tool to calculate the thickness factor for the inside skin. I used the baker's percents I earlier came up with together with the pan size and shape (10" straight sided). I assumed that the inside dough skin went up the full 2" depth of the pan. I entered values for the thickness factor until I got a total dough weight for the inside skin of 16.87 ounces (2/3 x 25.3 ounces). That value turned out to be 0.12637 and the dough formulation for the inside skin was as follows:
Flour (100%): Water (50.9375%): IDY (0.99843%): Salt (2.4609%): Olive Oil (1.98413%): Sugar (1.7578%): Total (158.13876%):
 302.48 g  10.67 oz  0.67 lbs 154.08 g  5.43 oz  0.34 lbs 3.02 g  0.11 oz  0.01 lbs  1 tsp  0.33 tbsp 7.44 g  0.26 oz  0.02 lbs  1.33 tsp  0.44 tbsp 6 g  0.21 oz  0.01 lbs  1.33 tsp  0.44 tbsp 5.32 g  0.19 oz  0.01 lbs  1.33 tsp  0.44 tbsp 478.34 g  16.87 oz  1.05 lbs  TF = 0.12637

Note: Assumes a 10" straightsided pan with a depth of 2" and that the inside dough skin is pressed up to the top of the pan without overlapping; the corresponding thickness factor = 0.12637; no bowl residue compensation
A thickness factor of 0.12637 strikes me as a reasonable number although I can't say whether that is what Zachary's uses for the inside dough skin since I have never tried a Zachary's pizza.
For the outside skin, using the remaining 8.43 ounces of dough (25.316.87 = 8.43), and assuming a diameter for the skin of 10", I calculated a thickness factor of 8.43/(3.14159 x 5 x 5) = 0.107. In my opinion, that is far too high. If I had to guess, if the outside skin is to be almost diaphanous, you would perhaps want to use a thickness factor for the outside skin of something around 0.050.06. You might also make the skin larger so that it can be more easily secured to the inside skin. So, for example, for a 12" outside skin with a thickness factor of say, 0.055, the weight of that skin would be 3.14159 x 6 x 6 x 0.055 = 6.22 ounces. This is something that will require some experimentation to get right.
Now, if we fast forward to the 12" size pan you plan to use, and assuming that it is straightsided and 2" deep, then the dough formulation for the inside skin might look something like this:
Flour (100%): Water (50.9375%): IDY (0.99843%): Salt (2.4609%): Olive Oil (1.98413%): Sugar (1.7578%): Total (158.13876%):
 405.68 g  14.31 oz  0.89 lbs 206.64 g  7.29 oz  0.46 lbs 4.05 g  0.14 oz  0.01 lbs  1.34 tsp  0.45 tbsp 9.98 g  0.35 oz  0.02 lbs  1.79 tsp  0.6 tbsp 8.05 g  0.28 oz  0.02 lbs  1.79 tsp  0.6 tbsp 7.13 g  0.25 oz  0.02 lbs  1.79 tsp  0.6 tbsp 641.54 g  22.63 oz  1.41 lbs  TF = 0.12637

Note: Assumes a 12" straightsided pan with a depth of 2" and that the inside dough skin is pressed up to the top of the pan without overlapping; the thickness factor = 0.12637; no bowl residue compensation
For the outer skin, I would use a calculation such as described above. For example, you might use a 14" outside skin. Using 0.055 as a thickness factor, the weight for the outside skin would be 3.14159 x 7 x 7 x 0.055 = 8.47 ounces. For the ingredient quantities for the outside skin, I would use the expanded dough calculating tool at
http://www.pizzamaking.com/expanded_calculator.html. The Dough Weight option would be used with the 8.47 ounces (and the same baker's percents as before). That would give us the following:
Flour (100%): Water (50.9375%): IDY (0.99843%): Salt (2.4609%): Olive Oil (1.98413%): Sugar (1.7578%): Total (158.13876%):
 151.84 g  5.36 oz  0.33 lbs 77.35 g  2.73 oz  0.17 lbs 1.52 g  0.05 oz  0 lbs  0.5 tsp  0.17 tbsp 3.74 g  0.13 oz  0.01 lbs  0.67 tsp  0.22 tbsp 3.01 g  0.11 oz  0.01 lbs  0.67 tsp  0.22 tbsp 2.67 g  0.09 oz  0.01 lbs  0.67 tsp  0.22 tbsp 240.12 g  8.47 oz  0.53 lbs  TF = N/A

Note: Assumes a 14" outside skin with a thickness factor of 0.055; no bowl residue compensation.
To get the total dough ball weight (including the dough for the outside and inside skins), you would add together the ingredient quantities for both skins when you make the dough. You would end up with a total dough batch weight of 31.10 ounces (22.63 + 8.47 = 31.10). If you are ever able to get the proportions for the inside and outside skins right, then you might be able to use the deepdish dough calculating tool with the stuffed crust feature.
With respect to the stuffed crust feature of the deepdish dough calculating tool, I'd like to mention that there is an error in that tool. I discussed same a while back at Reply 2 at
http://www.pizzamaking.com/forum/index.php/topic,12462.msg118833/topicseen.html#msg118833. In your case, I think you should try to get the thicknesses of the two skins where they should be and then reconstruct everything so as to allow you to use the deepdish dough calculating tool with the stuffed feature for the entire dough. Of course, you should feel free to play around with your own sets of numbers in the tools to get to a better set of output values.
You raised a question about what goes above and below the outside skin. From the instructions given in the article you referenced, it seems that everything goes below the outside skin except for the sauce and grated Parmesan cheese. They go on top of the outside skin.
If you proceed, I will be interested in seeing how a hydration of around 51% works. That is a fairly dry dough. I mention this only because I tend to be suspicious of most recipes that I see in articles that are attributed to particular pizza places. I have seen so many errors and misstatements in the past, whether intentional or unintentional, that I am suspicious of just about all such recipes. In the case of Zachary's, I also wonder whether a V.P. and COO of the company is the best one to discuss their recipes.
Peter