Please tell me how to pray witr namaz when dua qanoot will be used.

Check the following link for details reg witr prayer

http://www.sahih-bukhari.com/Pages/Bukhari_2_16.php

If you want to know the best way to offer the witr prayers, see a video for how it is offered in Masjid al haram in makkah during ramadan. The best and accurate information source.

Dua - e - qunoot is recited in the second half of the third rakaat