Separate them before it results in death. The female (larger one) is generally the aggressor. Acclimation box is best and i would give the aggressor a time out, not the one getting beat up
Female clownfish are much more dominant than their male counterparts. They greedily try to eat most of the food that gets into the tank (which is one reason the males don't grow as large). They will often aggressively protect their "home", whether that be an anemone, a nesting site, a clay pot or the entire fish tank. If it attacks your hand when you're trying to clean the glass or it won't let any other fish near its spot, you most likely have a female clownfish.
Often, the female will barely let the male eat and sometimes will almost control where in the tank the male is allowed to go. This will go on until the male submits or is killed by the female.
