I got it by following way.Please let me know if there is any better way of doing it via SSIS transformations.

1.Truncating and filling records from CSV to staging table.

2.Putting look up on staging table and filling records in base table.(matched rows go for update and unmatched rows for insert)

3.To deal with duplicates I put an Execute SQL Task in control flow and there I have built query to remove duplicates rather updating the same record if it is there as per my requirement.