As Randy said, you do it only once, it's independent of driving modes. To be more precise, there's a different tables/maps for different modes, for example Boost, Throttle "response" etc... but all modes are affected, there's no stock anymore
Until you flash the stock map of course.
p.s I did noticed change in Eco mode, especially with throttle response, but that might be different depending on engine/WG type etc..