When diagnosed with more than one autoimmune disease, what are some ways to distinguish the roots of the symptoms and how to manage them appropriately?

MS symptoms are often similar to other autoimmune disease symptoms as well as medication side effects. At times it is very difficult to distinguish why a symptom is caused, for example fatigue when having MS, Connected Tissue Disease, Hashimoto's, Depression, and taking Alendronate (Risedronate) for Osteoporosis. The preface of my proposed question is, does it matter what causes it? If it does, how to you deal with the cause and if it continues more than 'normal', what are the best approaches to handle it and who should you reach out to?