Hi ad-bwdc-ca,
It's nice to see you in Community. Welcome! QuickBooks Online enables you to manage your sales tax and record payments, or refunds seamlessly. However, to ensure you're recording the GST rebate accurately in your books, I suggest speaking with an accounting professional. They will provide their expertise and best course of action to ensure your records remain aligned with governments regulations, for non-profit organizations. If you don't have an accountant, you can follow this link to locate a ProAdvisor in your local area.
Please don't hesitate to reach back out with other questions. We would be happy to help!