If you are registered for GST/HST, then you have to submit an GST/HST return, which is separate from your income tax return. TurboTax Online & CD/Download can’t do an GST/HST return. However, if you are a Full Service customer, your TurboTax Expert will prepare both your income tax return and your GST/HST return. You can also submit your GST/HST return through the CRA using your My Business Account, which you can log into here: https://www.canada.ca/en/revenue-agency/services/e-services/e-services-businesses/business-account.html
You’ll need to provide your HST number on your self-employed tax return so that when the CRA processes it, they will quickly know that you have an GST/HST return.