After you have created the New/Extra Batch, you may proceed to process the payroll accordingly.
Refer to the following for steps:
Instructions
Main Menu: Run > Select the Batch you would like to process > Run
Employee Selection Section: Select Employee(s) for processing > Next > Yes Proceed
Adjust Salaries and Payment Section: Add Payment Item accordingly
If you are processing Extra Batch prior to Main Run, the system would include Basic salary as part of processing.