I gather he has sorted out his tax return up to April 2009? He therefore knows the exact amount of tax he owed for the year. This will include any taxes already deducted at the source by the person paying him.
Tell him to ring up his tax office and request a reduction in the amount owing for this current tax year's payments on account - there's a form to fill in, they'll send it out if they can't do it online due to him being a CIS person. All it means is that you have to estimate what tax you think you'll end up owing after the tax year we're in now, after deducting CIS stuff, and they will then reduce payments on account accordingly. The font on my PC has gone awfully weird and tiny, so I apologise if I've misspelt anything,.