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Lupus is an immune disease that can attack many internal organs and tissues. The classic parts of the skeleton that can be affected by the inflammation of lupus are the peripheral joints - the joints away from the spine, such as the small joints of the hands and feet, the wrists, knees, elbows, ankles, and shoulders. Lupus commonly causes arthritis in these joints. The spine is generally spared from the inflammation of lupus.
Lupus can cause neck and back pain, however, because muscles can become inflamed by lupus. Furthermore, the muscle pain syndrome called fibromyalgia that can cause pain in these areas is commonly associated with lupus. Moreover, cortisone medications that are frequently needed for lupus can weaken the bones of the spine, leading to breakage (fractures) of vertebrae. Also, a rare complication of lupus that involves inflammation of the spinal cord (transverse myelitis) can be associated with back pain.
Finally, neck and back pain most frequently result from injury or wear and tear (degenerative change with aging). This is true in the general population and is also true for patients with lupus. However, there are many causes of pains in these areas, ranging from organ disease (such as kidney problems and others) to disc herniations. It is not possible for me to know what the exact cause(s) of your particular neck and back pain are. For this you must consult your doctor.