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Normally the workers UTR and CIS Verification number should be shown on the invoice. This can be done with an Invoice template - please contact InTime support for assistance with setting up an invoice template.
Payment
It is possible to make payment to the CIS workers either from InTime or InPay but we would normally recommend making payment from InTime by generating a BACS payment file for the CIS Self Bill invoices. You then do not need to generate BACS payment files for the CIS payroll in InPay.
HMRC monthly submissions will need to be made for the CIS workers from InPay. This is done from the Processing - HMRC Submission menu. Select the "CIS Monthly return" type.