Not as an automated process, but, even simpler, all you need to do is produce a report showing gross income for the relevant VAT quarter and multiply the total by your Flat Rate %.
Enter the result in boxes 1,3 and 5 on your VAT return form and the gross income sum in box 6 on your VAT return. We would recommend you keep a copy of the workings and a copy of the completed VAT return before sending, and then file all paperwork in your business records for future reference / your accountant, etc.
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