I'm not saying that this is how it should be done but... IF I had one, I would mount my laser on my rifle where I would want it, turn on my laser bore sighter and sight it in at 25 yards. Basically put both dots on the same spot at 25 yards.
My irons and my red dots are zeroed at 50 yards, the only reason why I would use my laser would be for faster acquisition in CQB situations. That's when a laser would come in handy, and since in CQB situations, most targets will probably be closer in distance. Hence the difference in yards from zeroing my irons/red dot to a laser.