What does it mean if I have terrible headaches everyday that medicine can't help? All in my neck and shoulders as well

Several things. Could be a tension headache, cluster headache or cervicogenic headache. Definitely worth seeing your doc for this. I would recommend a do who uses omm to treat headaches. In the meantime, i would suggest starting a headache diary. Here's a helpful link to get you started. http://www.headaches.org/for_professionals/headache_diary.
Sounds Cervicogenic. When people have neck pain, shoulder pain and associated headaches, the cervical spine is usually the trigger. Most often the underlying joints of the neck are either acutely inflammed or arthritic (chronically inflammed). Treat the neck to get the other sites to calm down. Medication management, injections of the soft-tissues, joints and sometimes disc zone of the neck can help a lot.