Definitely wait til ammonia and nitrite is at zero.The algae could be using up the trates so thats a good thing.After my tank cycled,I added a cleanup crew,within a week they had pretty much cleaned up eveything(rocks,sand,glass).In fear of my cleanup crew starving to death,I'm adding seaweed sheets every few days.
Its ugly, I know but it will get better.BTW,I said it already but great rocks,looks kinda like my Uaniva.