You can create back pay transactions either through Back Pay or the Global Back Pay function in Update Pay Rates and then import your normal transactions.
To apply the new rates to the current transaction, you must update the employee's pay rates before entering or importing the transaction. You can do this by:
If you use Back Pay (Payroll, Transactions, Processing), tick Apply new rates to employee on process within the rate tabs.
If you use Global Back Pay in Update Pay Rates (Payroll, Transactions, Processing), either use Pay Class Pay Rates in Update Pay Rates or Edit the Pay Classes.