All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
The Witr prayer is a desirable Sunnah and the supplication of Qunoot is a desirable Sunnah as well and not an obligation. Reciting chapter Al-Ikhlaas (i.e. Quran 112] three times in Qunoot instead of supplicating is a religious innovation. The 'Ishaa' prayer is 4 Rak'as only and the Witr prayer is not part of it; for more benefit on how to perform the Witr prayer, please refer to Fatwa 83303, and to Fataawa 88201 and 83220 on how to make up the missed Rak'as which one missed with the Imaam.
Allaah Knows best.