Do you use your "real" name? Or do you use a diminutive based upon your first or middle name? Do you use a nickname?
In the notes section of your genealogy software indicate why you used the name you did. Future genealogists and relatives might like to know why you used it.
I have always used Michael, never "Mike." This is largely because my family always called me Michael and mother always said "if I had wanted him called 'Mike' I would have named him 'Mike.'". And I always thought Mike Neill sounded too short to be an actual name--at least to my ears--probably the result of being half German where every name needs to be somewhat long and have a lot of consonant sounds.
I started using my middle name because when I started my job, there was another guy in town named "Mike Neal" who was always getting arrested for one various thing or another. That was a way of distinguishing myself.
I know my great-grandmother Neill never used her "real" name of Francis--she used Fannie on everything, Francis appears ONLY on her birth record.
But jot this sort of thing down in your genealogy notes. Someone in a hundred years may want to know and you won't be around to tell them.