Create a payment for the appropriate supplier.
Once the payment is confirmed you will be brought to the Allocation menu. This menu will list any unallocated payments and unpaid bills.
Select the appropriate payment and enter the amount to be allocated in the Allocate payment box beside the appropriate bill.
The amount overpaid to the supplier will remain as an unallocated payment and can be viewed on the Money > Unallocated cash menu. It can also be allocated to future bills from this menu or the overpayment can be refunded.