Quran recited in the three Rak‘ahs (units of prayer) of Witr:
14- It is a Sunnah (Prophetic tradition) to read in the first Rak‘ah of the three: {Exalt the Name of your Lord, The Most High} [Quran 87], the second: {Say, "O disbelievers} [Quran 109], the third: {Say, "He is Allah, [who is] One}[Quran 112] and sometimes add:{Say, "I seek refuge in the Lord of daybreak} [Quran 113] and {Say, "I seek refuge in the Lord of mankind} [Quran 114]
It was also proved that the Prophet, , once recited a hundred verses of the Chapter An-Nisaa’ in one Rak‘ah of Witr.
Supplication of Qunoot:
15- One should recite the supplication that the Prophet, , taught his grandson Al-Hasan ibn Ali, may Allah be pleased with both of them, which is:
"O Allah, guide me among those You have guided, grant me security among those You have granted security, take me into Your charge among those You have taken into Your charge, bless me in what You have given, guard me from the evil of what You have decreed, for You decree, and nothing is decreed for You. He whom You befriend is not humbled and he whom You take as enemy is never honored. Blessed and Exalted You are, our Lord. There is no refuge from You except to You.”
One may ask Allah The Almighty to confer blessings and peace upon the Prophet, . (There is no harm in adding other permissible, good and valid supplications).
16- There is no harm in reciting the supplication of Qunoot after bowing and adding other supplications such as invoking against the disbelievers, and asking Allah The Almighty to confer peace and blessings upon the Prophet, . It is permissible to pray for Muslims in the second half of Ramadan as this was proved to be done by the Imaams in the caliphate of ‘Umar, may Allah be pleased with him. It was mentioned in the above narration by ‘Abdullaah ibn ‘Ubayd Al Qaari, may Allah be pleased with him, "They used to invoke against the disbelievers in the middle saying: 'O Allah, destroy the disbelievers who are trying to prevent people from following Your path, who deny Your messengers and who do not believe in Your promise. Make them disunited, fill their hearts with terror and send Your wrath and punishment against them, O Lord of Truth)."'Then, he would ask Allah The Almighty to confer peace and blessings upon the Prophet, , pray for Muslims with as much good as he can, then seek forgiveness for the believers.
After that, he would say, "O Allah, it is You whom we worship, to You we pray and prostrate, for Your sake we strive and toil. We place our hope in Your mercy, O our Lord, and we fear Your mighty punishment, for Your punishment will certainly overtake the one whom You have taken as an enemy." Then, he would say Takbeer and fall in prostration.
What to say at the end of Witr:
17- It is from the Sunnah (Prophetic tradition) to say at the end of Witr (before or after Tasleem), "O Allah, I seek refuge in Your good pleasure from Your Anger, and in Your forgiveness from Your punishment, and I seek refuge in Your mercy from Your wrath. I cannot count the praise due to You. You are as You have praised Yourself."
18- When he makes Tasleem, he would say, "Glory be to The Sovereign, The Most Holy" (thrice), elongating the syllables and raising his voice the third time.
The two Rak‘ahs after Witr:
19- One may perform two Rak‘ahs (after Witr if he wishes), for they are proved to have been performed by the Prophet, . Rather, he said: "This travelling is exhausting and difficult, so after anyone of you prays Witr, let him pray two Rak’ahs. If he wakes up, this is fine; otherwise, these two Rak’ahs will be counted for him."
20- The Sunnah is to recite in them: {When the earth is shaken with its [final] earthquake}[Quran 99] and {Say, "O disbelievers} [Quran 109].