You’re correct that all HMRC receive is the final adjusted numbers, not the original calculations or the amount by which each box was adjusted.
A VAT return is just a special kind of journal - the calculated box 3 total gets debited to sales tax control and credited to vat liability, and the calculated box 4 total gets credited to purchase tax control and debited to vat liability, which leaves the vat liability nominal equal to the calculated value of box 5. Manual adjustments work similarly, but they use the “manual adjustments” nominal for the contra entry.
So suppose you work out that you need to adjust box 1 down by £1000 and box 4 down by £750, so reducing box 5 by £250. This will adjust the vat journal by debiting £250 to vat liability and crediting the same to manual adjustments. Now you know that in this case the £250 difference needs to go back to the sales and purchase tax control accounts (because you’re removing items that have already been accounted for in the previous return), so to get everything straight you would need to make a new journal with
- 250 debit manual adjustments
- 1000 credit sales tax control
- 750 debit purchase tax control
QuickFile can’t do this automatically because exactly where the adjustments need to be moved to depends on why you’re adjusting, which is something only you can answer.