Hello.

If I understand correct Origin charged You for their margin when paying the invoice.
If this is a kind of bank/transaction fee for you than when paying Purchase invoice you register Payment following way

1. create new Payment and enter invoice you payed, and leave Sent amount as full invoice amount (you payed this invoice in full, in your example 351,75)

2. than you mark the line with invoice with blue by clicking on its number and choose Line option Add Bank fee (you use right click of the mouse to see the menu options)

3. system adds extra row for Bank fee where you can enter the charge amount and you OK the Payment.

In above scenario system will register Purchase invoice as fully payed as well as book Origin cost on account specified for Bank fees in Purchase ledger > Settings > Account usage Purchase ledger.

If you do not do bookkeping in Standard Accounts and you do not need to register in the system Origin charges than you just follow above point 1.

In case you overpay Purchase invoice, on Payment record you can change Sent amount manually to the one on your bank statement and OK record. System will allow it and in Purchase Ledger report system will show this invoice with - amount that is overpayed.

Best regards