Over the years I've noticed that most safety conscious, conservative beginning pilots tend to land on the far side of the runway, which I think is a good thing. The plane doesn't go there accidentally, you subconsciously head it over there because of a natural respect for that spinning prop.

Over time you can bring the plane closer, but only when you have complete control. You have to use the rudder to keep the plane lined up where you want it. I find it convenient to line the plane up on final to land much closer to me than I want it, and then use rudder to push it toward the center. In this way you are conscious of the actions you are taking to move the plane away from you, and realize you have control over the landing spot. Don't do this unless you feel comfortable with it.

As for flaps, they should be applied soon enough to help slow the plane down and to settle into a stable attitude, this usually means the base leg.