Does the software itself deduct HST from expenses or I have to manually deduct it before entering the amount for self-employed taxes?

If you are registered for GST and regularly file GST returns, you will leave all GST off of the entries on your personal return. If you are not registered, you will include the GST in your revenue and all expenses, but not list it separately.  You can view this info to see if you need to register and remit GST, if you are not doing so already.

https://www.canada.ca/en/revenue-agency/services/tax/businesses/topics/gst-hst-businesses/when-register-charge.html

Thank you for the clarification:)

@msinghnbf You're welcome!