We can set up a discount item, eawarner1. 

Yes, we can include the discount in our invoices by creating a Discount item. Let me show you how:

1. From the Lists menu, select Item Lists. 
2. At the bottom-right, click the Item drop-down and click New. 
3. Select Discount as the Type. 
4. Enter the discount details. 
5. Click OK to save. 

If we've already created an invoice, we can open and add the discount in another line item. The total amount is now with the subtracted discount. 

Here's an article that you can refer to when receiving invoice payments. 

Feel free to mention me in your reply if you need more help. Take care always!