Depending on the lights and if you have a sand sifting goby, I would recommend that you put it on the sand. They can also live on rock but their natural spot is on the sand.
John what do you have for lights and how many watts ? What are the dimensions of the tank ? Generally Brains do best on the substrate with low/moderate flow. If you have MH's then I would shade him from direct light otherwise they have been known to bleach.
maybe an overhang, scoot it underneath and see if it does better. I had a nice green open brain in my 180g years ago and it was only under 250w halides, 10k and it didn't even like those. Had to place it more in a cave or an overhang would work.