It’s something that’s been asked a few times on the forum. There’s no fixed way of doing it at the moment, but there are work arounds.
Check out some of these pages:
http://community.quickfile.co.uk/t/managing-cis-tax-taken-on-sales-invoices/1732/6
http://community.quickfile.co.uk/t/construction-industry-scheme-cis/317
http://www.qfaccounting.co.uk/index.aspx?q=CIS