Diagnosing these two diseases is tricky, which is why many people go from doctor to doctor for a long time before they finally get a diagnosis. Blood tests and the like are not much help - for instance, you could have a negative RA factor, yet still have the disease (I've had RA for 40 years, yet my RA factor claims I don't). Diagnosis tends therefore to be based not just on test results, but also on examination and presentation of symptoms as examined by a specialist in autoimmune diseases, i.e., rheumatologist.

The thing about chronic diseases is that you have good and bad days. Medication should ideally increase the good days to a point where you can live your life reasonably well, but they're still going to be times when you get sideswiped. However, if you feel uncomfortable with the diagnosis or your quality of life, you can discuss alternative treatment options await your rheumatologist, such as increasing the dose of the medication you're on or looking into other medications or if you want to get checked out again, just to be sure it is RA and Lupus, get a second opinion.

Good luck!