All you need to worry about is if your broadhead is on the shaft straight. It makes no difference at all, if the fletchings line up with the blades. (like KM said...how do you line up 2 or 4 blade heads with 3 fletch arrows?)
Tune your heads to your shaft, and you won't have any problems(assuming your setup is tuned properly). Also, the bigger the head, the larger fletching you may want to use. Most folks can use 4", personally I like 5".