I have had this in the past, where even after it saved, it simply took time to apply the changed number of items. I do not think you are missing a step. If you are doing it within the item menu, then you go into the item, go down to the variation, add the number to the field within the "on hand" column, click Done, then click Save. If you go through Inventory management, it should just allow you to add to the drop down on each item.
