I've found the best way is to just do it all at one time. Remove some water if you want, and just move all the rocks that you want to move around at one time. My clowns the last time that i did a rock shift, still ended up in the middle of the tank, but it wasn't a drastic change, just pulled down the wall and stacked on side higher.
Fish adapt, they will reorient to find new homes if it's drastic enough and wont be any worse for wear.