I have a very similar situation..I just got an ro unit, and I was trying to get alot of the water out so I could get rid of this reddish/brown crap all over the tank (ro water WILL get rid of the algae problem, BTW). I just did 10% water changes every couple days or so, or until I had enough produced by my ro unit. After about 3 weeks all algae was gone. I think if your fish are doing ok right now, then just do as would normally, and it will eventually all be out of there.