Although within the VAT settings area you can configure your VAT settings on a quarterly and monthly basis, it is also possible to create reports for the Annual Accounting Scheme for VAT.
Running the Return
To submit the VAT return for a 12 month period, you simply go to Tools and reports > General reports > VAT Management Reports > New VAT Report. Use the date fields at the top to select your reporting period, i.e. 01/02/2012 - 01/02/2013 > Re-Run Report.
The only options that will not be relevant to you in Settings > VAT Settings is the 'include VAT liability on overview screen' and ‘VAT period’ option. There is not a setting to enable annual account for VAT, so under ‘VAT Period’ choose either option. These options make no difference to your reports, and are only used for the ‘Include VAT liability on overview screen’ option.