I’m in the same situation as you, the epos records vat individually on each sales line. I get a report at the end of the day giving a breakdown by VAT rate (0%, 5%, 20%) of the net, vat, and gross totals but those figures are never the exact percentage due to rounding.
To record it in QuickFile I just create a single line invoice set to 20%, enter the net total from the epos report in the net column, then adjust down the VAT column to match the VAT total from the report. I then attach a copy of the report to the invoice in QuickFile as evidence of what I’ve done, and if we ever do get inspected the full details of every transaction are there in the EPOS backend - it doesn’t really matter that your master records are spread across different systems as long as you can point the VAT man at the correct records when he asks.
I then allocate payments to the invoice based on the Z readings, and hopefully the Z totals agree with the gross total from the VAT report.