Which is the best position for supplication in the Witr prayer—given the lengthy nature and the sensation of pain during prostration—and is it better to supplicate during the Witr prayer or during the Fajr prayer?

The best position for supplication (du'a) in prayer is prostration (sujud), based on the Prophet's (peace and blessings be upon him) saying: "As for prostration, strive in supplication therein, for it is most fitting that your supplication will be answered."

To overcome the discomfort of prolonged prostration, supplications can be distributed to other parts of the prayer where supplication is sunnah, such as between the two prostrations and before the taslim.

Regarding Qunut in Witr prayer, scholars have differed on its ruling, with various opinions: that it is not recommended, or that it is always recommended, or that it is only recommended during the last half of Ramadan. It is a permissible form of supplication.

As for Qunut in Fajr prayer, the imams have differed on its permissibility, and the prostration of forgetfulness (sujud as-sahw) is sunnah for those who omit it, according to some who hold it to be sunnah.

In summary, if one holds the view that Qunut is permissible in Witr and Fajr prayers, then there is no harm in performing it in both or in one of them.