Water evaporation is good, it promotes cooling!
I would not put covers on as they trap heat and somewhat prevent light from penetrating the water. Plus they get messy and are a pain to remove and clean all the time LOL.
I would just invest in a simple Auto Top off to replenish the evaporated water, and just watch the tank temps.
I lose about 1-2 gallons a day in evaporation on my 90G, and I have a chiller.
HTH,
-Mike-