When I bought this house, the former owner had covered the filter and pump with a tarp. Last year, my first closing, the pool guys removed the pump and we put it in the shed. The filter was left in it's normal spot; I bought a small grill cover to cover it.
This year, the pool guys said that they'd prefer not to remove pump or filter, that they'd had better luck leaving the pumps where they are all summer, uncovered. They blew out the lines and did a lot of work to close but I wasn't sure what to do about the pump.