I can share a situation that I recently encountered?  Our G/C paid for sand that was delivered to his jobsite earlier than we were on the job.  So I owed that G/C the cost of the sand. 

I made a Credit Memo under the Customer-Job (G/C) and applied it to the G/C's Invoice; which placed the cost of the sand in COGS and reduced the amount that the G/C owed to our company.  Hope it helps.