QuickBooks Point of Sale & QuickBooks Enterprise

In setting up items, I have used service, and pointed them to correct revenue and COGS accounts. We want to be able to use the "actual vs estimates" report which is at the item level. Before I have put the revenue items in the estimate, and then put in the estimated costs by item, and had a 100% negative mark down for each item, so that net for estimate is only the amount to bill client. This approach brings estimated costs to above report, to compare to actuals. However, not working as the cost estimates are being reflected in revenue section of actual vs estimates report at amount before 100% negative mark down. Doing something wrong – help!