What is the purpose of a second set of 5v and ground wires found on many basic Arduino breadboard projects?
With that circuit it will work fine either way. With larger projects, though, it makes sense to have two (or more) sets of rails available so that the closer one can be tapped off of instead of bringing power all the way across the board with discrete wires. So you put the wires in place on the far side (or near side, it doesn't usually matter terribly which), and you just never get around to removing them.