I have operated both once a day and twice a day and I have not seen a difference between the two so I don't think it matters all that much. If FC were to drop to a critical level, mixing the water some might make a difference. For skimming, it can make a bit of a difference since debris drops on the pool all the time but I would not get too concerned if you can run the pump only once per day.

Also, as long as FC levels are appropriate, the time of day should not matter much either but if I had to pick a time, it would probably after sunset. That would be the most logical to mix up the water and even out the FC levels overnight.