We are the US distributor of a product produced overseas. For some legacy customers, we must buy goods from supplier and resell to customer, at same price. Then we invoice the supplier for our sales commission. Quickbooks desktop doesn't allow us to invoice a supplier/vendor, so  we set up both vendor and customer entities for this supplier. 

However, now the supplier is asking us to subtract the sales commission from their bill payment, and also send them an invoice for that sales commission.  

How can I create this invoice, and use the eventually "received" payment to reduce the vendor bill?

For example. Customer orders $1000 product. We purchase and deliver $1000 product, invoice the customer $1000, then create a 10% commission $100 invoice to supplier's customer account, mark it paid and use that to reduce payment on the $1000 vendor bill, to $900.