Juvenile Arthritis

My 4 year old was diagnoised at 16 months with JRA. We are fighting side effects of medicine and I don't know what to do. Is there a safe medicine for her? Our rhuematologist said that the methotrexate was safe. Now she has sores in her mouth and suffers from a folic acid defiecency. I have learned now to do my own research not to just take the doctors word for it. Now that I am reading up on the medicines I am scared to death for my daughter's health. I pray everyday that we will find a balance between treating her arthritis and her having quality of life and that her treatments won't effect her quanity of life.