VAT Flat Rate Savings Entry ??

Hello

I am on the flat rate vat scheme with a rate of 6.5%.

As quickbooks does not show in your profit and loss the income made from the diffrence of 20% charged and 6.5% given to Hmrc and just shows income minus 20% vat i am getting slighty confused on the following.

Currently to work out my income tax i take my total income add the 20% vat paid then minus my flat rate at 6.5% and then obviously minus all my expenses but what i find confusing is when you submit your quaterly vat through quickbooks which calculates the flat rate correctly but then add a journal entry that is labeled savings from flat rate and its classsed as an income but its a odd number not corosponding to what i make or earn from the Flat rate.

So at present i am having to ignore that income entry and do the above calculations to get the correct amount for self assement purposes.

Any advise if this is correct and or the purposes of the savings by frs entry when submitting which at the moment is throwing my income number off and making it very confusing.

Regards