Just looking at a VAT Notice (733) on Flat Rate, and came across this ‘Common Error’ (7.7 on the link)
VAT exclusive figure is put in box 6, meaning that the flat rate is applied to the net, rather than the gross turnover
As it says there, Box 6 should be the gross figure.
Also from notice 700/12:
Box 6 total value of sales
Enter the turnover to which you applied your flat rate percentage, including VAT. You should also include the value, excluding VAT, of any supplies accounted for outside the Flat Rate Scheme, such as the sale of any capital goods on which you have reclaimed input VAT, and reverse charge transactions. Also include any amount you have entered in box 8.
Hope that helps clear it up for you 