Because of how unique and powerful the weapons effects are against specific units, I try to only place the AFP in a single suit unit. The commander is the best choice because he can then take the other weapons that keep him adaptable to any situation.
I have used the CIB several time and I am always underwhelmed. I jump up ad down when I kill a terminator with an ap1 shot, but I just cross my arms when I cause one ap4 wound and the marine makes his save.
The only thing I like about the CIB is the one I converted, so it still sees the light of day when I am feeling flashy.