Paying a CIS Subcontractor

I am trying to pay a subcontractor who also has a credit on his account. The invoice has gone in under 6000 (NC) as he is a CIS subcontractor (Gross) and a credit under the same NC, both tax codes T9, but when I try and pay them, I have the following:- When allocation credits against invoices the net payment must be zero for all transcations within the same VAT code" - not sure what this means?
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    You need to allocate the credit note against the invoice first.

    So select "Allocated CIS Credits" then you need to pay in full the credit note & then put the same sum against the invoice so the balance comes to £0.00 then pay it that way.

    Once you've done that, go back into the payment & pay the remaining balance.

    It's a pain I know!