I am assuming that you are referring to a GEDCOM file. Please let me know if I am wrong.
The best option for updating a GEDCOM on the Family Site is to import it into the Family Tree Builder and publish the results to your Family Site. You can retrieve the Family Tree Builder from this page: http://www.myheritage.com/FP/Company/products.php .
To import, open FTB and go to the File menu and select Import GEDCOM.