Reconciling old VAT3 payments with bank account?

I’ve been working on moving my accounting information over to a new BulletHQ account as I never properly reconciled my data against my bank account.
The only remaining issue is to reconcile VAT3 payments. The problem I have is that when I generate the VAT3 reports in my new account, the values are different to what I actually submitted to Revenue (in some cases significantly).
My plan is to continue generate the VAT3 returns and then when I’m reconciling them with the different bank account transaction for that period, to use the “auto-adjust” button.
Is this the way to go?

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