Any current employee or employee that were terminated after the nominated date in your MicrOpay database will be included in ESS. There is no option to exclude individual employees.
The Directory will show all employees in ESS, and there is no option to exclude specific members from the Directory. If you have employees that you don't wish to appear then you would need to deny access to the Directory for all employees. This will also prevent members from being able to review the Leave Calendar for all employees. To do this:
Go to Settings, Roles & Permissions.
Select the Role you want to update.
Click Edit.
Under Global change, the permission for View Directory to Deny (red circle with a white cross).
Click Save.