There is an adjustment tab in the VAT return that can be used to change the figures that are submitted to HMRC.
From the main menu go to the VAT Management.
Select VAT DETAIL tab and BUILD DATA at the bottom of the screen.
Go into the MTD ADJUST.
Select the box you want to amend by clicking on the pad and pencil icon.
When this comes up you will need put the figure in you want to add or minus off that value.
Select the Tick icon after.
A reason box will come up, put in why you are doing the amendment.
Select the Tick again and then the figure to go through the VAT return will amend to include it.