This is very easy along as you remember that the form is wrong. and you ignore the instructions (As long as you are not trading with the rest of the EU).
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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