Evaporative coolers work by exchanging the entire volume of the air inside your house with cooled air several times per hour. Unfortunately, the cooled air is more humid than outside air, so if you do not allow the air inside your house to be exhausted to the outside (by partially opening windows/doors at the distal corners of the house), the humidity will build up. You MUST allow for circulation/exchange of the air otherwise the house will get damp, and feel like a swamp.
As to saving water by cycling the pump on/off, that depends the degree of water saturation you are getting to pads now. If they are totally saturated, and a lot of the water is dripping out of the bottom of the pads, you might be able to reduce the net water flow without reducing the cooling efficiency. If the pads are already mostly dry, and little or no water is running out the bottom of the pads, then any further reduction in water flow will reduce the cooling efficiency.