Go to Items.
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Press Modifier Groups in the upper right corner
Press the edit icon to the right of the modifier group you want to assign quantities to.
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In the popup window, enter the quantities in the empty fields to the right of each modifier, under QTY.
Scroll down and press Save Changes.
Assign Stock Quantities to Modifiers in Mod Groups
In order to assign stock quantities to specific modifiers, the modifiers will have to be in a modifier group. You do not need to enable stock management in the backend.