What Name do You use and Why?
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.