LKK you are right.. dua-e-qunoot parhni chaiye in third rakah but after surah-e-fatiha + another surah + takbeer.
Its like you started third rakah with surah-e-fatiha and then read some surah (like surah kausar) and then do the takbeer Allah-o-Akbar.. now you read dua-e-qunoot or rabbana ataina.. and go to ruku