how I can manage two different time zone in same application?
Sorry, what do you mean with “manage two different time zone”?
one employee is in UAE and second employee is in Pakistan, how they will check in/out?
how I can select the time zone for both the employee?
You have misunderstood the use of time zone in this case. You don’t need to set multiple time zones, only one will do.
Kindly visit the online user guide to understand more about this.