The seconds don't matter for alignment. You just need to have minute and hour hands lined up at the date change (if the movement has a date), if no date it doesn't matter where you line up the hands. Think about it, you can have the hands line up right at the 12:00 marker no matter where the seconds are. 12:00:15, 12:00:30, etc... Just make the hands line up at 12:00, that's all there is to it.