Hi BRegehr,
Welcome to Community! QuickBooks Desktop enables you to file and pay your sales tax effortlessly. I'd be glad to assist!
You can use the Tax Agency Report to File and Pay. Using the Pay Bills or Write Cheques feature could cause a negative impact on your sales tax reports and other areas of your books. To ensure you're recording the payment accurately, here's a detailed guide, for your reference.
Please don't hesitate to contact us if you require additional assistance. It would be our pleasure to work with you directly and help you accomplish your QuickBooks goals as soon as possible.
Feel free to get back to us here, if you have other questions. We'd be happy to help!