If the old payroll system is STP enabled, then the easiest way to migrate would be to complete two STP submissions, a Final STP submission in the old payroll system and a Final STP submission in the new payroll system, at the end of the financial year.
The employee will receive two reports from the two systems in their MyGov account.
If the old payroll system is not STP enabled, you will need to import the figures as pre-accumulated data into the new Payroll system, depending on how the new system handles pre-accumulated data this may or may not be added to the STP report, if not you will need to submit a PAYG Payment Summary instead for the total figures for the financial year.
The new payroll provider should be able to help with this.
Don’t forget you will also need to import pre-accumulated entitlement balances regardless of which method you use.
A good payroll provider will assist with setup and migration.