There are holistic methods of dealing with pain and your various ailments, but the problem is that, in many cases, it would result in you having to take a whole battery of supplements, vitamins, etc. to try to sort it all out. Even then, the long term impact of such things is less-than-documented, and the short-term benefits are often debatable or dubious.
Now that the disclaimer is out of the way, there are many wonderful, holistic methods of assisting you. I would speak to your doctor or other such professional about your desire to see if holistic and alternative methods might assist you with your troubles.
Perhaps try acupuncture to assist with the pain and stress of it all; it may even be covered by your parents' insurance. Professional reiki practitioners in your area might also be worth a shot. Many people have had positive results with reiki when dealing with pain and the auto-immune issues that you list. Though, again, I wouldn't expect miracles. Depending on the availability in your area, it also might be worth your while to consult with someone versed in Chinese medicine, or Ayurvedic healing as well.
Beyond all of this, perhaps ask your doctor about speaking with a dietitian about diets that can help you reduce inflammation, which would assist you with reducing pain and other symptoms from the fibromyalgia, arthritis, and cysts. They may also be able to recommend herbal supplements for this. The migraines and the like are quite possibly symptomatic of the lupus, or the stress you're under in general. Stress relief techniques such as meditation (as well as the acupuncture or reiki) may help with them.
As someone who is well acquainted with auto-immune issues, pain, and the medicine cabinet that goes with it, I can honestly say that there are no surefire ways fix these problems. I wouldn't necessarily give up on the conventional medical methods prescribed either. Do your research about them, and don't rely on hearsay. Everyone (EVERYONE! grr) has some miracle cure, miracle diet, or miracle advice that they are going to tell you about, without ever having researched the illnesses themselves, or ever having undergone the treatments, diets, etc. themselves. What's worse, the same methods that work for one person may not work for another. Read the actual medical studies. Read the actual research that has been done. Be patient as you try medications and holistic methods as often they take some time to yield results. And, bottom line, do what you can to try to do it all in a manner that is comfortable and feels right to you. And when people start pushing their miracles on you, tell 'em to get lost.