First off, the design of these is genius. They have slits on the side for dogs with dew claws, they fit nicely, they clean easily, and the holes throughout keep dog's feet ventilated but also protected from hot pavement and other surfaces.
I would recommend storing them with tissue or something stuffed inside the shoes. Because of the material, just storing them on a shelf doesn't work because they sometimes cave in and become hard to put on your dogs fit. But a little toilet paper or sock ball...