yes! it will make a difference. the end of the pigtail needs to sit right around the drain hole. This will put the end of the spring out the farthest from the body of the car (closer to the wheel).
no, it probably won't hurt anything. However, most rear springs tend to sit a bit higher than the fronts, even under the nest of circumstances. Unless you really want it to look jacked up in the back, install them the correct way.