When generating an invoice, you would have options to add discounts, finance charge, late fees etc. However, please note that if any such items are to be added to a previously generated invoices, it should be done using Invoice Change function instead of directly adding the main invoice (This function would be available end of March 2018).
Additionally, the addition of these items on the invoice does not affect its GST/HST. For example, if you add the discount to your invoice as a line item, it would not cause a reduction in taxes. See article below which seems to indicate CRA does not permit changes in taxes due to early-payment discounts, finance charges etc.
If you simply want to reduce fees and reduce associated taxes, you have two options:
You can enter a negative value time card to reflect a reduction in fees and this will reduce taxes charged on your fee.
You can use “Change Invoice” function (This function would be available in March 2018) to reduce Invoice fees and taxes. If the invoice was already issued and you are writing-off / making changes, only this option should be used as using this option.