If the witr is tahujjud prayer, as you hold, then why do we offer it with isha and can you please tell me the method of offering it? Is it three raka'at with dua-i qunoot in the third raka'ah? If one misses isha prayer for some reason then does he have to make qaza (delayer performance) of witr like we do for obligatory prayer?
Since witr is part of tahajjud prayer it is necessary for those who start offering tahajjud during the night. Those who offer it with isha indeed follow the views of the jurists who take it to be second to fard (obligatory).
We believe that the Prophet (sws) allowed those who could not get up during the late night especially during Ramadan to offer tahajjud before going to sleep. This relaxation was later on taken as general ruling. For method of offering the witr please go through the article: Optional Prayer
Since witr is nafl (optional) there is no need to offer the prayer afterwards. For detail discussion on qaza prayer please refer to: Qaza Prayer