"User specified" means that you want the operator to enter the costs when the item is sold. "Standard cost" will be used if that is the costing method specified for the Control Account set for the specific inventory item. You tell Adagio what costing method to use for the item with the Control Account Set.
The actual cost that is passed to the general ledger is based on the costs of the goods as they are received and whether you are using "LIFO", "FIFO", or "Moving average" costing. If you have selected Standard Costing, then the costing variance from the calculated average cost will be posted to the cost variance account. These are specified with the item category.
So, when you say that the items have "costs of $0.00", what number are you actually referring to? If you are looking at the Inventory Valuation report, then this is based on the costs of items that have been received. If you have not received any items, then there will be no costs recorded.
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Andrew Bates