How I can only affect certain Employees when I Publish?
Publishing affects all positions, employees, and shifts for that week in that account, so only one or two Managers should normally have permission to Publish. Those Managers should be sure any other Managers are finished with their portion of the schedule before Publishing.
If you are scheduling multiple locations or departments in one account and no employees are shared across locations/departments, you can create separate WhenToWork accounts for each location or department. This will allow them to be scheduled and published separately.