I can only tell you what I did to get service connected for my headaches. I kept a headache diary (I used Excel). I noted that headaches pain level 5 and above were recorded. Listed what I had to do for the headaches (medicines, lie down, cold compress, go to dark room etc.) and most importantly, what the headache was linked to, what was happening right before I got the headache. In my case it was anxiety. In your case, you would need to note where else you have pain. Finally, how the headache effected my life, work and personal. I know longer have excel, but my diary is attached.
I sent in a copy of the diary with a letter saying I requested disability for headaches secondary to anxiety. Just like that, nothing fancy. I brought a copy of the diary to the C&P and offered a it to the examiner. She declined and told me I did a good job describing cause and effect. The diary helped me do this as well.
I recommend doing this for anything that you want to claim service connection for so that you can have 1) a history and 2) be able to review before you go to the doctor or C&P
Forgot to mention, I also gave a copy to my primary care physician. Just keep it updated. I got 50% for my headaches. HeadacheDiary.xls