If you charge an amount for late payment of a bill, the GST and QST must be calculated on the amount shown on the invoice before the addition of the late-payment charge.
You charge $5 for late payment of a bill of $100. In this case, the GST and QST must be collected only on the amount of $100, even if your customer actually paid $105 for the item.
When the amount you bill the customer is already net of the early-payment discount, you must charge GST and QST on the invoiced amount.
You send a customer an invoice with instructions to pay $108 if payment is made by March 23, or $118 if payment is made after March 23. Even if the customer makes the payment after March 23, you must charge GST and QST on the amount of $108.