What is a skillful way to meditate in the midst of a migraine headache? When the Bod-hisattva Quan the Am, who has been such a source of
  inspiration of peace workers in Viet- nam, saw into the reality of the
  five aggregates giving rise to emptiness of self, she was liberated
  from every suffering, pain, doubt, and anger. -- The Miracle of Mindfulness, p. 48


I have been practicing mindfulness for less than a year. I have had some deep experiences and found benefit. However, when I have a migraine headache my mindfulness feels completely useless. 

Any guidance or any good resources that would teach me to practice my mindfulness in the midst of a bad headache would appreciated.
Theravada Buddhist Answer based in the Burmese method as taught by the Ven. Mahasi Sayadaw.

The following method is based in Vipassana meditation. This type of meditation is characterized by taking reality as an object of meditation, meaning that one directs attention towards the most apparent object in the present moment.

In terms of a migraine attack one might focus on the pain, nausea if present, a feeling of lightheadedness or ones reaction towards those objects. 

One would note whatever object is most predominant and change object when another object becomes predominant. One notes the pain by mentally and slowly saying to oneself "pain, pain, pain". This is done while keeping attention on the object. One notes in order to create clear comprehension about the object, so to not fall into either liking or disliking of the object. 

When this is done repeatedly over a period of time the mind will come to see the pain as merely an object. One will come to understand that the pain is not a problem. Instead its our own reaction to the pain that creates suffering for us.

For more in-depth information on the method in relation to dealing with pain, I recommend the following video teachings given by Ven. Yuttadhammo:


Ask A Monk: Dealing With Pain and Using Suffering as a Vehicle for Enlightenment
Ask A Monk: Pain
Monk Radio: When Pain Becomes Unbearable


He also made a booklet, which is available here.

May you have a fruitful practice.