RE: No room on site for three pins?
Definitely shoot a few hundred shots in it to settle the rigging. But the fact that you can't get a pin low enough in your sight suggests that your anchor point is too high and your peep is too low. For reference consider that an average distance between nocking point and peep is between 5 and 6", depending on drawlength, ATA and string angle at full draw. But this should get you in the ball park.
Try raising your peep and lowering your anchor. Goodness man, on my hunting bow I can get 80 yards and still have about 3" between the arrow and the sight.