Is this the case that you have a customer who is also a supplier?
If so you can create a journal entry to contra the payment between the two accounts.
To do this, go to the + Icon > Journal Entry and enter the following details:
1) Correct the date
2) On the first line, on the category drop-down select your 'Creditors' account, enter the payment amount in the debits box, and choose the supplier under 'Name'
3) On the second line, on the category drop-down select your 'Debtors' account, enter the payment amount in the credits box, and choose the customer under 'Name'
4) Save & close the journal entry
To apply the journal entry to the invoice payment, open the invoice and select 'Receive payment' then check the journal entry under 'Credits' on the Receive Payment screen.
Thanks
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