Depending on the story I usually swap perspectives from Hero to Hero, Hero to Villain, etc. If Iâ€™m writing from the hero perspective and he/she is using their alter ego then I usually keep the alter ego name e.g. â€˜â€œI canâ€™t believe the cops werenâ€™t there sooner” said Baxter as he looked out the window.’
However as soon as the mask is on I refer to him in their Hero title as everyone else will. The fact that heroes do refer to themselves as their Titles even when they are in their alter egos is present in some animated series. In Batman beyond Bruce says to Terry that he knew he wasnâ€™t going crazy because the voice that spoke to him (Later revealed to be Shriek) called him Bruce. Terry questions why was that strange to which Bruce responds I donâ€™t call myself Bruce. This hints at, heavily, that Bruce refers to himself as Batman.
So in Super hero stories I keep in mind that the hero is who they really are and the alter ego is the facade they put on to the world. So while writing speaking parts for heroes I use their Hero names instead of their birth names.
Everyone above me has just as good a point as I do. Good job fellas and good luck on your story.