If payment to cra done manually, how to update quickbooks?

Hi there, 

Welcome to the Community. QuickBooks is the go-to program for small business looking to simplify their accounting. I'll be happy to show you how to record a tax payment. 

Here's how: 

1. Go to Taxes and select Sales tax.
2. Go to Filings tab, locate the tax filing from the Filed section.
3. Select Record payment option from the View summary dropdown.
4. From the Refund to dropdown, select the account you're making the payment from.
5. Select the Refund Date.
6. Select the outstanding tax payment and adjust amount as needed.
7. Select Add interest/penalty if you need to add one to the filing.
8. Select Record payment at the bottom.

For more info, please check out the following article: Manage sales tax payments in QuickBooks Online. 

Let me know if this info helps. I'll be a message away in case you have other questions. Otherwise, I wish you a great rest of the week!