It isn't absolutely necessary that you use the preferment dough calculating tool. If you can find and use an existing dough recipe that calls for a natural starter/preferment and can get the recipe to work, then that might be good enough for your purposes. The advantage of the preferment dough calculating tool is that it allows you to devise your own dough formulations where you can alter just about any of the baker's percents of the ingredients permitted by the tool. You can also use the tool to convert a dough formulation using commercial yeast to one using a natural starter/preferment. Moreover, because of the way the tool was designed, if you enter the proper numbers for the starter/preferment into the tool, the risk of ending up with an incorrect hydration should be quite low.
With respect to the way the water percent is calculated for the starter/preferment, if you look at the preferment "box" at the middle of the preferment dough calculating tool (http://www.pizzamaking.com/preferment_calculator.html
), you will see a "Note" that tells you how to calculate the number that applies to the water. So, using Matt's numbers of 40 grams of water and 60 grams of flour as an example, the number to enter into the tool is 40/(40 + 60) = 40/100 = 40. It is so simple, a caveman can do it.
For background purposes, I think you might find it helpful to read this thread where I discussed a hypothetical example of adapting a basic Lehmann dough formulation to use a natural preferment rather than commercial yeast: http://www.pizzamaking.com/forum/index.php/topic,6969.msg59839.html#msg59839
. However, just because you can use the preferment dough calculating tool to create a dough formulation, does not guarantee you success. Member mooncrickett apparently discovered this as he explained in the thread at http://www.pizzamaking.com/forum/index.php/topic,10578.msg93820.html#msg93820
and more recently at http://www.pizzamaking.com/forum/index.php/topic,11434.msg104331.html#msg104331
There are also other limitations to the preferment dough calculating tool. One is the limited number of ingredients that can be used with the tool. It provides for the basic ingredients of flour, water and salt, commercial yeast (but only if used to supplement the natural starter/preferment, such as the Jeff Varasano dough formulation, for example), and sugar and oil. The latter two ingredients were included for those members who wish to make Neapolitan style pizzas in standard, unmodified home ovens and find it useful to add some sugar and/or oil to the dough formulation (e.g., a Caputo dough) to improve the performance of the dough in such an oven. I should also mention that the tool does not provide for milk, vinegar or baking soda--some of your recent favorite ingredients. It also does not provide for using exotic ingredients like yak vomit (scalded or unscalded), which I have heard through the grapevine you are considering as a way of getting more flavor in your Lehmann crusts at market.