[Edratman]

If you have enabled renaming in the initial setup screen, then open the comanders stats view and type "r". That will open a box enabling you to rename the commander.

You cannot rename a pretender or prophet under any circumstances.

I find renaming more useful for designating special attributes, like a mage who has gotten lucky and picked up 2 additional astral paths as "4 Astral", and other things like that.