So, I was always curious about how a head girl or boy is chosen. Does it matter if my character used to be a prefect? For example, if I had the sixth year character Bob who was the best student of his year, and he was a prefect, would he become the head boy because he is the best student? Or that doesn't matter? Also, let's say that Gideon becomes the head boy next year, will someone else take the Ravenclaw male prefect position?

I'm pretty sure the answer is something obvious, but meeh.

On prefect, short answer is no.

On head boy, I can't speak for Charming, but in Canon it was all 'round deserving - not just best in school but of good character. Though sometimes non-prefects could get the spot (James Potter comes to mind), this would not have been the norm.