I plan on putting this sight on when my new/used bow arrives. But my question is there are 3 sets of holes to mount to a bow. Does it matter what holes you use when mounting it?

It's all personal preference, really.

You will notice though that, sometimes, the further your pins are away from the bow the more accurate you'll shoot. This isn't the case with everyone, but for some people that's just how it works. Try all the distances to figure out which works best for you.

Personally, I shoot best with it mounted using the middle set of holes. However, I don't center my pins in my peep when I shoot, I line the rim of the peep on the rim of the sight.

That sounds like a good idea to center the peep around the sight it self. I think that is something I will deffenitly try. Thanx.

...and you might as well copy and paste the rest of his post in here because I agree with it as well. Something else to consider is how far the sight sticks out in front of your bow. I tend to like to have it fit snug underneath the upper limb pocket for protection.