If you want the overpayment carried as a supplier credit, delete the reference to the specific invoice on the payment form. Leave Accounts payable and Supplier A. If a payment is allocated to a specific invoice, it remains tied to that invoice, causing it to be overpaid. If not allocated to a specific invoice, Manager will allocate it to the oldest unpaid invoice.
If necessary to control things more tightly because of other invoices, you can split the payment into two lines. Allocate one to the specific invoice so it is paid in full. Allocate the balance only to the supplier. The total of the lines will still equal the amount paid.