If you are changing the salary of an employee mid-way through a period, you will need to manually calculate the pay for the number of days paid on the original rate and the number of days paid on the new rate.
In this example, the employee is paid monthly and on an annual salary of £20,000 to the 15th June. From the 16th June they will now be paid £25,000. The calculation for 15 days on a £20,000 annual salary is £833.33 and the calculation for 15 days on a £25,000 annual salary is £1041.66. The basic pay for June would be £1875
When you process the pay for the employee, replace the basic pay with your manual calculation.
Once you have processed pay for this transitional period, edit the employee from the Employees > View menu and update their hourly rate or gross annual pay to their new wage (in this case, a annual salary of £25,000).