Look at the official documentation: https://github.com/orientechnologies/orientdb/wiki/SQL-Update#example-3-add-a-value-into-a-collection. So:
1) If your record has RID #13:33:
update #13:33 add company.employees = #4:6
2) The same (https://github.com/orientechnologies/orientdb/wiki/SQL-Update#example-4-remove-a-value-from-a-collection):
update #13:33 remove company.employees = #4:5
3) With set you cannot have duplicates, so if you add the same item multiple times, it's simply ignored with no errors.