Both. When you change the flap setting the trim will likely change. Do not change at low altitude the first time until you see how the plane reacts. Takeoff in whatever setting you desire, gain some altitude and set the trim as normal. Then change the flaps up or down (whichever they were not) and see how the plane reacts. Change may be small or large, this is why you have altitude which = time to react. Re-trim as desired. Get used to moving the flaps around at different flying speeds and seeing the planes reactions. Again it may be small or large. Small & large are also a relative terms depending on experience. Some planes are also "neutral" meaning that you won't notice ANY change but this is rare.
Oh - you are re-trimming the elevator, not the flaps.