Some ingredients such as boxes and packaging may only be used on a to go order vs. an in house order. You can manage this with the "Ingredient Usage by Order Type" feature.

This article assumes you've already mastered the basics of adding ingredients to items, and you've navigated to the Item Ingredient set up screen. 

To limit the usage of an ingredient by order type, place your cursor in any cell for that ingredient. Press the “Set Order Type” button at the bottom of the screen

Just uncheck any order types for which you do not want this ingredient deducted. This will apply to all size/style combinations for that ingredient line.   The ingredient will now appear in green to indicate it has order types selected.