Does the puzzle have to land on a certain side, or can it lay on any side when solved? If so, what kind of penalty do you get for making it land on the wrong side?
It doesn't matter which side is on top (see http://www.worldcubeassociation.org/regulations/#magicsolving G4a)
I solve the magic and master magic with the right side on top, but I saw already competitors who solve it with the other side on top. I think it depends on your method and the kind of magic you use which case is better. Some magics work mirror inverted than the others.