I dont think there is a "right" way to do this. if you are referring to a hydro system, i personally prefer to set the timer to water them once the lights come on, sometime during the middle of the day, and about 2 hours before the lights go off.
Water and nutes travle back down and into the soil at night. I would think the best time to water is just b4 sun up or lights on. When sun or lights are about to come on the water and nutes travle back up the stalk and into the plant. This is what iv been told by multi people and sorces. If i am wrong please feel free to let me know so i can learn.