Witr Prayer can be performed in a number of ways, among which three rak`ahs are offered, but they are split into two parts; salaam is said after the first two rak`ahs, then following a slight pause, one stands up and prays another rak`ah followed by salaam.
As for the Qunoot, Sheikh Sayyed Sabiq states, “It is part of the Sunnah to supplicate with Qunoot in the Witr Prayer during the entire year. Ahmad, At-Tirmidhi, An-Nasa’i, Abu Dawood, Ibn Majah, and others narrate that Al-Hassan Ibn `Ali said, ‘The Messenger of Allah taught me the (following) words to say in the Witr Prayer: ‘O Allah, guide me among those whom You have guided. Grant me safety among those whom You have granted safety. Take me into Your charge among those whom You have taken into Your charge. Bless me in what You have given me. Protect me from the evil that You have decreed, for You decree and nothing is decreed for You. And there is no humiliation for whom You take as a ward. Blessed and Exalted are You, our Lord.'”
At-Tirmidhi grades this Hadith as Hasan, and says, “… Nothing is known from the Prophet concerning Qunoot more authentic than that.” Commenting on its status, An-Nawawi says that its chain is Sahih. Ibn Hazm has some reservations about its soundness, but says, “This Hadith, although it is not one that can be used as a proof, is all that we have from the Prophet, and a weak Hadith is dearer to me than mere opinion.” Ahmad says this is also the view of Abu Musa, Ibn Mas`o
od, Ibn `Abbas, Al-Baraa’, Anas, Al-Hasan Al-Basri, `Umar Ibn `Abdul`aziz, Ath-Thawri, Ibn al-Mubarak, and the Hanafi school. This, An-Nawawi says, gives credibility to the report.”
Qunut can be recited immediately before or after ruku`. It is permissible to recite the qunut aloud in any of the five daily Prayers at those times when Muslims are faced with calamities.
Sheikh Sayyed Sabiq adds:
“It is permissible to make qunut before ruku` (bowing), or it may be recited after straightening up after the ruku`. Humaid said: “I asked Anas, ‘Is the qunut before or after the ruku`?’ He said, ‘We would do it before or after.’” This was related by Ibn Majah and Muhammad ibn Nasr.
If one makes qunut before the ruku`, one should say “Allahu Akbar” and raise one’s hands to the ears before reciting the supplication, and similarly say “Allahu Akbar” after the qunut, and then bow. This has been related from some Companions. Some scholars hold that it is preferable to raise one’s hands in supplication during the qunut, while others disagree.
As to wiping the face with the hands after the qunut, Al-Baihaqi writes, ‘It is preferred not to do so and to confine one’s self to what the early generations did. They raised their hands but did not wipe their faces during the Prayer.’