Ship and Bill transactions - how to set up?

I have a client that has two types of orders -- direct from their own inventory, or direct from the manufacturer.  For the latter, they receive the order from the customer, notify the manufacturer, and the customer pays the manufacturer and receives the product directly from the manufacturer.  The client then receives a commission from the manufacturer for the sale.  There are variable components that make up the commission, but that's secondary right now...first I have to figure out how to set up this type of sale so that it doesn't show up as the customer owing money, it doesn't