Black Widow supplies an owner's manual DVD with their bows (I just got a new BW longbow), and it gives a very detailed explanation by Ken Beck of tuning a bow. After watching that a couple of times, this whole issue became very clear.
What Rob said above is accurate; broadhead alignment has nothing to do with feather alignment. But that 'wing' (broadhead) on the front of the arrow is going to catch the air like a sail if the arrow isn't tuned right. If your arrows are going to porpoise (up/down) a bit when they fly, then perhaps a two-blade could be aligned so that it is vertical at the point in its flight when it would first catch that air, before the feathers straighten it out. For left/right (spine) tuning problems, if the broadhead is more horizontal at the point where it would catch that air (before the feathers straighten it out), then that horizontal arrow movement could, theoretically, have less effect on arrow flight.
A couple of years ago I had a terrible problem with arrow flight and 3-blade heads, before I knew anything about tuning. I ended up rotating a broadhead slightly and shooting it, until I found where the broadhead shot exactly like a field point. I rotated all my broadheads identically and get great arrow flight now (with those specific arrows, length and weight, on that bow). I shoot with a homemade arrow sight on my BW recurve, and so could very accurately compare a field point with the broadhead.