Are you talking about this support topic?
This is an import tool, it will not try to resolve if an entry is a duplicate of one or not. So each time you run an import, every entry is imported as new.
Not sure I understand what you mean by “the managers name and the actual employee that answers to that manager shares the same field on the site” and what the issue is. You’ll have to explain in greater detail.
NOTE: This topic will also be moved to the CSV Import forum within 24hrs.