You should either choose one, or interchange them based upon the situation.
For example, a superhero script, would have the same character sometimes listed by their superhero identity, and sometimes by their real name. This isn't always a hidden identity, for instance in the X-men movies. There are times just based on his presence and actions when Wolverine is listed as Wolverine, and sometimes Logan.
If your character is going to have times when he is in a military situation, and times not, I would suggest calling him by Rank and Last name when in the military enviroment, and by first name when he is not.
If it is a consistent enviroment (war story or such), it would depend on the character. If it is the main character, i'd list him by his first name for the most part. A supporting character it would be better to list them by their rank and last name, Especially if they are superior officers.