Having a migraine after an adjustment or cracking the atlas sounds scary. Maybe, it's letting the signals through the nervous system through that were restricted before the adjustment and it's causes the headache? I had a friend who would have headaches after getting his neck adjusted by the chiropractor afterwards. You may want to consult a doctor about that to make sure you aren't doing any damage when cracking. I don't know if other's can do it. I'm sure there are some out there who can.
Sorry, I should clarify: I've had a migraine after an adjustment from a chiropractor - never from doing this Atlas crack myself. The migraines I got after the chiropractor were from this one chiropractor I only saw twice (my regular chiro left the practice). This new guy used to work on athletes apparantly and he wasn't used to working on smaller women (I'm only five feet tall). When he adjusted me he would like, WIND up and then "WHAM" bring all his weight down. It was too hard. I felt sick afterwards and got a migraine both times I saw him….... I've had a slight headache after I crack the Atlas myself but never a migraine from it. When I went to my regular chiropractor (not the "sports medicine" guy) I would often have a slight headache after I left from the adjustment.