'There are special rules for sales which span the change of rate. If you provided goods or services before 1 January 2010 and raised a VAT invoice after that date you can choose to account for VAT at 15 per cent. You don't need to tell HMRC if you do this'
Here is a link that should explain everything that anyone should understand.
It is basically saying that the business can do whatever he/she likes.
Sorry about that!
Have you tried cashflow manager? I know in my last job we used Cashflow Manager to do the VAT Returns for clients. It is quite a simple product to use and I think it may suit your business but it can be quite fiddly.