@acris no, that’s not the way of doing it. Doing so will also map the buttons in-game incorrectly.
@PanJanDrum the truth is that there is still no easy way of changing the controls in EmulationStation. The only thing easy to change is the controls wihtin retroarch’s menu (swap A and B inside retroarch), but that’s not exactly what you are asking and I don’t remember the name of the entry to change either (it should be self-explnatory though).