1. Create a new account,  for example Purchase Discount,  create it under revenue or other income in your chart of account.

2. For supplier payment go to Accounting > Supplier Payments > Click Create >enter the supplier name for Supplier  > enter the full amount before discount for Total   and  etc 

3. System will auto pick a or some outstanding payments, but you are allow to change the Amount

4. Change the Amount to the discounted amount, a Difference Amount will appear 

5. At Payment Options  change to Reconcile Payment Balance , Counterpart Account and Counterpart Comment  will be populated.                     

6. Select Purchase Discount  at Counterpart Account 

7. Click Save and Validate