Once upon a time a master bowyer and champion archer (my dad) once told me to line my 2 blade heads up flat, perpindicular to the string. Here's why: He and I both build our arrows the same way- when gluing the nock on we put the grain flat, i.e. perpindicular to the string. This is to help line the arrow's grain in the strongest direction for combating archer's paradox (the bending of the arrow around the shelf of a non-center cut bow). When gluing on a broadhead, you want the added weight (and force during a shot) of the blades of a 2-blade head lined up in that same direction-- flat, with the strongest direction of the grain. This will keep the arrow flexing as little as possible during the shot, which will aid in accuracy or consistency.
Now, that being said- if you shoot 3 blade heads, carbons, or aluminum arrows then it really makes no difference as long as your broadheads are all lined up the same to remain consistent.
Hope I confused you less,
-Vig