I'll help you add the employee's earnings in the calculation of their pensions. Can you also tell us if you're using Advanced Payroll or Standard Payroll?
If you have Advanced, follow these steps on how to add a pay category to the pension scheme:
Go to the Employees menu and proceed to the Payroll Settings section.
Click Pension Settings.
Add all required Pension Scheme details if you haven't added anything yet.
Click Add, then scroll-down to the Contribution Plans section.
Check the box for Calculate pension on qualifying earnings.
Go to the Applicable pay categories field and add the earnings.