The first step is to set up a GST pay code. Go to Setup > Pay Codes and add a new pay code.
Now add the new GST pay code to the default pay codes for the relevant employees. under Setup > Employees, edit the employee, go to the Default Pay Codes tab, select GST and press the Add button. The GST will now be added to their pay by default, but will be ignored for the witholding tax calculation.
If the employee receives other non-taxable allowances (for example, a travel allowance) on which GST is charged, these will need to be entered GST inclusive, as the GST pay code shown above will only add GST to gross earnings and taxable allowances.