Use Lookupstage to decide whether to insert or update. Check this link for more info - http://beingoyen.blogspot.com/2010/03/ssis-how-to-update-instead-of-insert.html
Steps to do update:
Under Custom properties select SQLCOMMAND and insert update command ex:
UPDATE table1 SET col1 = ?, col2 = ? where id = ?
map columns in exact order from source to output as in update command