Welcome to the Community space, @Michelle I. I'm here to help you reconcile the old returns in QuickBooks.

Since you already submitted the transactions manually, you can manually reconcile the old vat returns in QuickBooks. However, I'd still suggest contacting the HMRC first and verify if they received the old returns that you manually send to them.

To manually reconcile the transactions, here's how:

1. Go to the Accounting menu and select Chart of accounts.
2. Find the account you’re reconciling and select Account history
3. Click the transaction to expand the view.
4. Select the box in the tick column until you see an R. This manually reconciles the transaction.
5. Click Save.

For more details on how to reconcile an account, see this article: Reconcile an account in QuickBooks Online.

Upon sharing the steps above, I'd still suggest contacting your accountant. They can provide further guidance with the setup and provide more expert advice in dealing with this concern.

Once done, you can start paying your current tax liability. These articles will guide you through the process:

• Submit a VAT return in QuickBooks Online
• File your VAT return and record tax payments in QuickBooks Online

​​Tag me in a comment below if you have other questions about VAT in QuickBooks Online. I'll be sure to get back to you. Take good care.