Greetings, @jalee.

You can automatically apply discounts customers invoice once you enable the Discount feature in QuickBooks Online. Let me guide you on how to do it.

1. Go to the Gear Icon.
2. Choose Account and Settings.
3. Select the Sales menu.
4. Go to the Sales form content section.
5. Mark the Discount feature.
6. Click Save.

Once completed, you can add a discount by percent or by a specific amount. 

You can use this article for more detailed steps: Add a discount to an invoice or sales receipt in QuickBooks Online.

Please know that I'm only a post away if you have additional concerns in handling those discounts. I'm more than willing to help. Take care and have a great day!