Payslip details not reflecting as payments done but showing as balance

I have created some payslip for a couple of employees and it shows as not paid. Is there a section where I can create a payment for these payslips.

When you create payslip, the net pay to employee will become liability which should be cleared when you actually pay the employee.

To learn how to record actual payment to employee, see: http://www.manager.io/guides/payroll/paying-employees/