The best way of handling supplier discounts is to enter the appropriate supplier discount on each purchase receipt line. This results in the correct cost being recorded against each purchase receipt line. As a result the cost of goods sold and margin on sales that use the stock being receipted correctly reflect the true cost of the goods.
If supplier discounts represent a small part of the total cost of goods, there is a shortcut that may save time but causes some level of error in the cost recorded on sales. That is create a non-stock product to stand for supplier discounts, put that product in a product category that correctly dissects the accounts used by that non-stock category. Then :
If you know the supplier discount at the point of entering the purchase receipt. Add the supplier discount at the end of the receipt then put the total supplier discount on that one line at the end of the purchase receipt
If you don't know the discount until you process the supplier invoice. Use the option to add a non-stock product that appears when you elect to invoice the purchase receipt