Hmmm, this is a good question. I'd be interested to know a proper way to do this as well. My only guess would be doing something along the lines of setting up an instance variable on a type of enemy, name the variable "dead" or something. Then, each time you kill one of them, check their UID and set their "dead" variable to true so, if dead = true --- destroy enemy.
I'd be interested to see what other people have to say too.