Originally Posted by CPH-Flyer

If you book it as a JAL flight number, there is no charge to select seats. If you book it as a AY flight number I am not quite sure what they do in terms of charge for seat selection. I don't know if you are looking at what you earn of points and qualifying points, there may be a difference between the JAL flight numbers and the AY flight numbers. But apart from earning and potential seat costs (which should go away if you have status) I don't really see much difference in booking one or the other.