"Upright", in egg-storing terminology, means with the larger end up (tapered end down). Upright storage helps retard spoilage because it maximizes the distance between the yolk and the egg's natural air pocket. That gaseous space is potentially the egg's most prolific breeding environment for airborne pathogenic bacteria, and the yolk is more perishable than the albumen (egg white). It stands to reason therefore that you must keep the yolk as far away as possible from the air pocket.
The second reason is more complicated. The egg yolk is lighter than the albumen and will rise to its surface unless restrained, which nature does with chalazas. These are the two cords attached on either side of the yolk designed to keep the yolk anchored in the center of the egg. The cord connecting the yolk to the smaller end is tauter than the cord tethering the yolk to the larger end of the egg. Consequently, the yolk does not float up as high when the egg is stored small end down.
