You can account for the loss of yield when preparing food items in two ways.
In the following example, we will use an onion and assume that when dicing, you achieve a 70% yield.
1) The first way is to use the yield % feature when entering an ingredient in a recipe.
In the example below, we set the recipe for mirepoix with different percentage yields for each ingredient (onion/70%; celery/75%; carrots/85%).
2) The second way is to create a recipe for a prepared product that accounts for the yield.
Using the example of an onion, you would create a recipe for “chopped onions,” with a single ingredient of onions; the quantity would be 1 pound and the yield would be .7 pounds (=70% yield).
The advantage of this option is that by setting the yield for a product after preparation you can use this recipe rather than the raw ingredient in other recipes and the yield will already be accounted for. Note that when you set the percentage yield in the prep recipe, you must set the yield for 100% in the recipe to avoid double counting the loss.
Here's a quick video reviewing this