You can run it during the evening/overnight hours if you want...I often do that when my pool water gets too warm in order to cool it off. The only real disadvantage that I can think of is that the temperature of your water may not be evenly distributed throughout your pool--you're going to have warmer layers on top and possibly warm "pockets" of water.

As far as total run time is concerned, you want to make sure that you're turning over your water at least once. In my pool that means at least 6 hours a day.

Janet