You should let your payroll department know when you start salary packaging as they may need to increase or recommence the amount of your withholding-tax deductions.
While each employer is different, in most cases your payroll department will be able to help you manage the process and changing your HECS/HELP repayments is quite simple to do. Your payroll department may have its own form or they may ask you to use the ATO's form Tax declaration form or Withholding tax form. Check with your payroll department first.
You should also seek financial or taxation advice if you're unsure.