Navigate to Settings > Accounting > Account codes.
Ensure that the Show in sales check box is ticked next to the Trade debtors account, to be able to create payments on account for a customer.
Also, ensure the Show in purchases checkbox is ticked next to the Trade creditors account, to be able to create payments on account for a supplier.
If you need to tick them don't forget to click Update at the very bottom of the table.
Navigate to Money > Bank accounts.
Click on the Explain link for the appropriate imported statement.
Click on the appropriate receipt or payment to begin explaining.
When explaining a receipt on the statement as a payment on account ensure that you choose the customer in the From field and the Trade debtors account in the Account drop-down list.
When explaining a payment on the statement as a payment on account ensure that you choose the supplier in the To field and the Trade creditors account in the Account drop-down list.
Once explained the payments on account will be ready to allocate against future Invoices and Bills via the Money > Unallocated cash screen. Click on the cash icon to allocate to invoices/bills.