Traditionally, you would put it in the DPS section, e.g.,
DPS1=Breath of Mysaphar|99
This would have it cast Breath of Mysaphar when the mob is at 99% health. You would likely put it lower in your DPS rotation and you might include a specific condition as to when you would use it. But the above will cast it pretty much everytime it's ready and you are in combat.