I have a character name question. Without giving anything away, I wrote a screenplay that involves one character that has to use two names during the duration of the script. You could probably say the same for when Superman or Batman are Clark Kent or Bruce Wayne. What I was doing was just using the name that the character is at that time. My question is – am I right? I figured since I give an explanation a head of time, that I could easily just call the character by his name or alias, and there would be no confusion.
You’re right in assuming that the most important thing is to avoid confusing the reader. Every script finds its own way of doing things, so there’s no hard and fast rule. If I were writing the next BATMAN, I suspect I would call use "Bruce Wayne" when refering to the awkward billionaire, and "Batman" when refering to the Caped Crusader. In a movie like this, the two different versions of the character rarely appear in the same scene, so it would probably be less confusing.
In the case of a movie like TOOTSIE, I’ve never read the original script, but I suspect that when Dustin Hoffman’s character is dressed as either a man or a woman, the script refers to him as Michael. When he’s in drag, his dialogue headers probably read like, "MICHAEL (as DOROTHY)" to make it clear which persona he’s playing at the time.
In the case of a movie like FIGHT CLUB (warning, spoilers follow), since the reveal that Brad Pitt and Edward Norton are actually the same person comes so late in the story, you would obviously treat them like two completely separate people.