Hello,
QuickBooks doesn't automatically apply a discount to a customer's Invoice or Sales Receipt but you can make it so the available discount shows on the Sales Form. First, in the Customer Center, go to that customer, click on the Additional Info tab, on the right add in the Custom Fields a Discount Available field and enter the discount rate you want to use for that customer.
Then change the template for the sales forms to add the Discount Available field on the forms so you can see it every time you bill that customer. Make sure to add the Sub-Total item line so you can then discount the entire invoice.