When you pay sales tax in QuickBooks, you are recording the payment against a specific sales tax period; you are not actually transferring money to the CRA.
You can also record instalment or partial payments this way.
QuickBooks will show you how much you owe and allow you to view your sales tax payment history. For payments, you must also make a payment directly to the CRA.
There are two ways to record a sales tax payment that will be applied as an instalment payment towards an upcoming filing period. From the Sales Tax page:
If you accidentally use one of these options to record a payment against an upcoming filing period when you meant to record it against an existing filing, the amount will display on your next filing instead.
To correct this inaccurate filing:
Once the adjustment is complete, you will have a sales tax adjustment in both the bank account and in the Sales Tax Payable account.
Adjust your sales tax liability
What happens after you enter a sales tax adjustment?