I thought I'd answer your query about waking with migraines because that's exactly how my migraines mostly emerge even after 45 years! Yes, that's right! I've had migraines for 45 years. I started when I was thirteen years old..so I guess you know how old I am now!
Anyway, I have gone to so many doctors, headache clinics, neurologists, naturopaths, etc. that I think I have a pretty good handle on what causes migraines. My neurologist says that the latest research shows that migraines are a result of a brain disorder. Of course, there are so many triggers that I don't know where to start with that.
When sleep clinics grew popular, I also spent the night at one of those to see if my sleep patterns, snoring, etc. could be the cause for my middle-of-the-night migraines. I found that I didn't have sleep apnea but the doctor told me that I go into deep REM sleep very late in the sleep cycle. I sometimes wonder if that has anything to do with triggering migraines.
I've never found a doctor who thinks that getting migraines in the night has any significance to the treatment of migraines. I bring it up all the time and the doctor just shrugs.
I've been on preventative medicines in the past (Depacote and Topamax). Migraine preventative medicines have nasty side effects, I feel. With Depacote I gained weight and became lethargic. With Topamax, I lost my appetite (got skinny) but couldn't concentrate anymore. In fact, sitting down to read was impossible because I just fell asleep.
I'm now trying to get more massages (to relieve tension) and exercise daily. That seems to help. Also, many migraine sufferers that I know say that botox is a real asset to migraine management.
Currently, my doctor has me on copius quantities of Riboflavin (B vitamin) (400 mg). Some migraine patients find relief after being on that quantity after 3 months. I take Amerge if I feel a migraine coming on. Sometimes I'll take one of those before I go to bed. Amerge has some preventative qualities and is not just for taking during an episode. The good thing about Amerge is that it will last for 12 hours. However, it could take a good hour to kick in so be sure to take it right as the pain starts.
Good luck. One thing is for sure for migraine patients: make sure you go to bed and get up at the same time, day in, day out. Migraine patients seem to thrive on a scheduled, predictable life.
Hope this helps.