I think the issue is not as much about diagnostics as it is about how to effect healing. A NUCCA or AtlasOrthogonal chiro may help define and help with getting started on a healing path but it also takes discipline to help the joints heal up properly. A Physical Therapist may also help if he/she has good gentle skills with the upper neck such as light traction with gentle joint mobilization. In my experience, pushing for range of motion prior to allowing the soft tissue to properly heal is counter productive.

A common way to help determine if head aches are neck related is by touching the bony parts behind the ears. If they are tender to the touch, it usually indicates muscle spasms radiating from the neck.

I have said this many times, sleeping and resting with good neck/head posture is important. Otherwise, the joints can be strained while the body is relaxed during sleep.