Working out and chronic diseases/pain

I have two autoimmune disease, one that attacks my joints and organs, and another that thickens my skin and organs. Because of this I have a lot of pain. I enjoy working out, but my brain always says "Hey! You can work out some more!" But if I do too much then my body goes into a flare and I can't even walk for a couple of days, so I know I have to work out while not doing TOO much. And this isn't just working-out soreness, it's lupus soreness.

Any one out there in a similar situation/want to keep me from going overboard?