It's great to see you taking full advantage of QuickBooks Online's powerful sales tax features. While the tax centre is designed with a focus on simplicity, there are several ways to take more advanced control of your books. I'll be happy to help you get this entered.
As long as you select Exclusive of Tax on your expenses, you should have no problem editing tax amounts in your subtotal (as long as the taxable subtotal is non-zero). Recording tax payments is best done on a specific, filed return from the Taxes > Sales Tax section. The New button here makes it easy to record an instalment if you haven't filed yet.
For additional control over the GST Payable account, selecting it on a Journal Entry unlocks the option to map amounts to a specific Sales tax line. I recommend reaching out to your accountant about this. They're experts about your company's financials, and are well equipped to help with taxes. You can easily invite your accountant as a user to approach this together. To search for a pro in your area, simply head to the My Accountant tab in QuickBooks Online then click on Find a pro to help.
Feel free to reach out any time! I'll be happy to further assist if you're able to share additional details about how this needs to affect your books.
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