Milo123,
Thanks for joining the Community. The program offers a flexible tax module and I'll be happy to share more information about making a one time GST/HST payment in QuickBooks.
First, you'll want to create an Expense type account in your chart of accounts called Non-Refundable Taxes (or something that makes sense to you). Then, use the Write Cheques function, payable to Receiver General, Non-Refundable Taxes as the account, enter the amount without a Tax Code. This method should not alter your GST Payable account.
For further assistance on this payment, I recommend speaking to an accountant. They'll be able to use their expertise to help view the books as they are with you in order to assist in formulating the best game plan so you can get everything correctly balanced, and the payments deposited. You can invite your accountant to QuickBooks Online so they can see your books by going to the My Accountant tab. You can also find an accountant near you that has experience using QuickBooks by clicking the Find a Pro to help button located in that section or click here to view our Find an Accountant website.
If you have any other questions, feel free to reach out here.