For this part, Yes, you control it: "I can't amend the qty before I copy to bill as that will increase the PO value incorrectly."
Of course you can and should change it on the Purchase Payment transaction, when things are not the same. Example: I order 10 and get 5. I don't put 10 on the bill; I change that to 5. Or, I ordered 10 and got 12, and am fine with that. The Bill or Check or Credit Card I make selecting, yes, this is fulfillment of the PO, has to be your Reality. The PO is a nonposting Planning tool. The purchase is the Real Event.
For you, only you know what this means. If you order Boxes from the supplier, and they know this is the retail box that is 5 to their own shipping carton, then you know you need to order 5 units as Boxes, and they will ship you one carton. The program doesn't control this. It's just your tool. You and your Suppliers control this.
You didn't tell us which program you are using. There are ways to manage Units of Measurement, such as One Carton = 5 Boxes, so that means you can manage that item with Either Unit of Measure. But you don't typically need that complexity. Just place on the order what you intend to buy and get. Then, show what you actually Purchased on the Purchase transaction (check or bill or credit card charge) because this is what puts it On Hand and in stock for this date.
