If you are speaking strictly of pain in your arms, including when laying in certain positions, you might consult a physical medicine doctor or even your primary care physician, who could prescribe anti-inflammatories (if you are able to take them) & refer you to physical therapy.
To have pain when you raise your arms above your head makes me think you may have some inflammation going on- whether it be tendonitis (I had this before, very painful), or bursitis (relatives have had this- also very painful and hurts to raise arms over head). The physical therapist could help you on range of motion excercises, when your body is ready for that, to try to strengthen the muscles in your arms, etc. You might see if a soft ice pak or moist heat helps with the pain any also. If you have acute inflammation, like when I had tendonitis, they might have you rest your arms for a certain period of time before starting physical therapy. They gave me a sling to wear. If they say you have bursitis, they may offer a steroid injection or to refer you to an orthopedist that can give them. You'll likely want to try something else first!
Also, as you lay in certain positions, you may find benefit from using a long body pillow between your knees and between your arms. If you could lay on your back if it is hurting to put pressure on the arm muscles & have a pillow tucked under the lower part of your legs or if you are blessed to have an electric hospital bed, to have the foot of the bed raised up, that might help some with the pain. If you wake up, as I have before, and find your arms are in a position that makes them hurt, of course, you'll want to fix that quick!
You should see a chiropractor. He/she will do a thorough examination of you including: range of motion, xrays, diet, medical history, etc. Therapy can include adjustment and alignment, electro therapy, heat therapy, massages, acunpuncture, diet changes and cleansing, etc. You will definitely benefit from it!
I would see a good chiropractor. Sounds like you might need to get an MRI. Once you know what is going on inside you can take it from there. Best of luck!!!!