There are two options to add the cost for a simple made-from-scratch ingredient.
Let's take lemon juice as an example. The first option is to add “lemon” as an ingredient, with the usage written in terms of "each" (e.g. "1 lemon" = "1 each"). Then, you would note that the lemon is juiced in the procedures section.
The second option is to create “Lemon Juice” as a sub-recipe. To do this, click the "+" next to “Components”. Then, enter the name of the sub-recipe you would like to add, in this case it would be “Lemon Juice”. Next, click the new sub-recipe’s name to create it.
Then, go into the “Lemon Juice” sub-recipe. Once inside, add lemons as the only ingredient and add the approximate yield.