Thanks for getting in touch.
It appears you've beaten me to the response. I would have done the same thing, by recording (through the banking page) the transaction as either an expense or Cheque to the Creditors account assigned to the supplier in question. This would assign the payment as a credit to that supplier which can then be assigned to any currently outstanding or future invoices you create for that supplier when you go to receive payment.
It's good to see that you were able to find this resolution on your end but if there is anything else we can help with, let me know and I will be back in touch