If I use a solar cover at night will it affect the skimmer, or if I'm using the solar cover should I just use the main drain while the pump is on? Logic tells me to use the main drain only....
The skimmer will still pull in water, just not off the surface very well. I would not think there is a need to change the valves just based on whether the cover is on or off. In fact, with the cover on (if during the day), you may want to pull the warmer water off the surface with the skimmer so that the heat mixes.
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