Hi Jill
Key invoice in full as normal. Key Credit note for amount of deduction but key to CIS tax nominal. When make payment to subbie link to invoice and credit note. (if I remember correctly!)
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Joanne
Winner of Bookkeeper of the Year 2015, 2016 & 2017
Thoughts are my own/not to be regarded as official advice,which should be sought from a suitably qualified Accountant.
You should check out answers with reference to the legal position