Convenient Store Inventory at retail and also tracking COGS

@pamphipps70 

"My boss wants me to keep track of COGS when I write a check to vendors - However, maintain inventory at retail to track against the merchandise sales."

With all due respect, your boss doesn't understand bookkeeping/accounting.  COGS has no relation to when you pay your vendors for inventory.  COGS is an expense account that records the cost of inventory at the time it is sold to your customer, regardless of when the inventory was paid for.  It would be great to expense inventory to COGS at the time it's purchased but the IRS doesn't like that and it's not proper accounting.  COGS is designed to match the expense of inventory to the same period as the revenue it generated. 

I'm assuming you're using QB just to track the cost of inventory but not the individual inventory items, correct?  If that's the case, when you purchase inventory from a vendor, it should be recorded to a temporary "Purchases" other current asset account.  Then, at the end of the week/month you need to make a journal entry based on the inventory value in your POS system.  Google "periodic inventory system".  That will help you get started.  Or, your accountant can make the month-end/week-end adjusting entry for you.