You just shift the circle traced by the crankarm upwards by 3mm.

(you actually shift it up by 3 when your foot is flat and less when it's angled. This effectively raises your pedal by 3mm on the downstroke and shifts the upstroke forward and up roughly equally. All of this extra motion is inefficient and is why you generally want your foot as close as possible to the pedal spindle. Imagine a 3inch cleat spacer and how much extra your foot would move)