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.
Your employees will receive a pay advice for each transaction entered, e.g. one for the back pay transaction and one for the normal timesheet transaction. You can generate the EFT file and pay advices for the back pay transactions prior to importing or entering your normal transactions. If you do this:
When you generate the EFT file for the normal transactions, the back pays won't be included in the files, as they've already been processed. You will need to add the total for both files together to balance.
As you produce pay advices at two separate points in your pay cycle, you will have two (or more) lines in STP Reporting. You will need to add the two together to balance.