Apply the first payment to the unpaid (open) bill as you normally do and then record another supplier payment and apply the second payment to the same bill. As this bill is now paid (or closed), you'll need to select the Include Closed Purchases option to see it. A debit for the second payment will be automatically created.
You record the payment using the Pay Bills window or by selecting the Pay Bills option in the Band Feeds window.
After creating the debit, you can settle it by receiving a refund or applying it to a future bill. For more information on settling supplier debits, see the AccountRight AccountEdge help (Australia | New Zealand).