I have produced a couple of invoices to a main contractor in the CIS scheme
He has had to stop tax @ 20% just on the labour content of the invoices.
I therefore have a cheque payment from him that is less than the amount invoiced.
How do I deal with the discrepancy in the amounts ?

Hi Alan,

The simplest approach is to add an extra line to your invoice with a negative amount - see this page for details:
http://www.solaraccounts.co.uk/help/cis-notes-for-subcontractors.php

Regards,

Thanks Mark