In "tuning" your bow you are attempting to get your arrow to fly as straight as possible out of your set-up, and achieve the optimal flight towards the target. For me personally, I'm a hunter that shoots a bow, vs. a target archer, and what I find works best for me is getting everything "eyeballed" as near set, and shooting to zero one pin at a given distance 15-25yds, depending on set-up. Once I zero that pin, make sure I'm not having fletch clearance/contact issues, etc, I move on to fine tuning. I'll perform a walk-back tune, in which you use the same pin and shoot at increasing distances, 15-25-35-40 and see if the arrow pattern trends in one direction or not, and tweak the rest in the direction you want that pattern re-align themselves and try again. After doing a walk-back, I screw on some BH's, spin them to make sure they are TRUE to the arrow, and BH tune. Again, tweaking the rest to get optimalgroupings in which my FP's and BH's hit the same spot.
This link
http://www.archerytalk.com/vb/showthread.php?t=539460gives a good demonstration of step-by-step BH tuning with a bow. It's been viewed over 35,000 times and with good reason.