If you are using only a few dough ingredients, like flour, water, yeast, salt, sugar, and oil, the Lehmann dough calculating tool at http://www.pizzamaking.com/dough_calculator.html
should be sufficient. If you are using more ingredients, the expanded dough calculating tool at http://www.pizzamaking.com/expanded_calculator.html
is the one to use. The deep-dish dough calculating tool at http://www.pizzamaking.com/dd_calculator.html
is unique to deep-dish doughs, and the preferment dough calculating tool at http://www.pizzamaking.com/preferment_calculator.html
is unique to doughs using natural starters/preferments.
What you should understand is that all of the dough calculating tools were designed to work with existing dough recipes that are already recited in baker's percent format or that can be converted to that format. As with any tool, you can put in any set of numbers and get a set of outputs, but that doesn't mean that the outputs will be usable. The tools don't work with recipes recited in volume measurements. The ingredients have to be specified in weights, which can then be converted to baker's percents.
Many people prefer to work with dough balls with a specified weight. In that case, the Dough Weight option of the tools is the one to select. Others like using thickness factors. They are related to the thickness of a dough skin; the specific values will vary from one style to another. For example, for a NY style dough, a typical range of thickness factors might be 0.07-0.105. Many members start with a value somewhere in that range and then adjust it up or down based on the results they get. When using the thickness factor method, the Thickness Factor option is the one that should be selected in using one of the tools. You will note that many members, me included, often recite the thickness factors used for their dough formulations (recipes). That should help you in scaling them up or down to meet your particular needs.
In the example you gave, the dough for a 16" pizza does not make two 8" pizzas. It is not linear like that. It is based on the surface area (Pi R squared) of the pizzas. To give you an example, the amount of dough to make a 16" pizza (R = 8) with a thickness factor of, say, 0.10, is 3.14159 x 8 x 8 x 0.10 = 20.11 ounces. For two 8" pizzas, the amount of dough using the same thickness factor is 2(3.14159 x 4 x 4 x 0.10) = 10.05 ounces. As you can see, the weights are not the same. For two 12" pizzas, the amount of dough using the same thickness factor is 2(3.14159 x 6 x 6 x 0.10) = 22.6 ounces. As you can see, that is closer to the weight of dough for one 16" pizza. Actually, the dough for a 16" pizza can be used to make two pizzas that are about 11.31", or about 11 1/3". For practical purposes, you can view that as being about 11"-12". Fortunately for you, all of the calculations are embedded in the tools. You just have to enter the correct values.
As for determining how much vital wheat gluten to add to a flour to yield a blend that has a target protein content of another flour, the best way to do that is to use member November's Mixed Mass Percentage Calculator at http://foodsim.unclesalmon.com/.
If you look at the items in the pull-down menus, you will see several popular brands of flours and vital wheat gluten. If a particular item is not listed in a pull-down menu, you can use the % data entry blocks below the pull-down menus. If you have a particular example in mind that you would like to test out, try the calculator. Let us know if you have difficulties using it.