I am pretty sure that if the company turn over is above the VAT threshold, everything charged to or by the company is liable to VAT, which includes the charges you mention.
Personally, regardless of the members experiences of running businesses, I would employ the services of a decent accountant, it may cost you a few extra quid each month but at least you'd know where you are every month and when the Customs and Excise come calling, you shouldn't have any major problems.