Kids/YA book about a boy with magic powers who goes to a magic school with courses split into three (?) branches (NOT HARRY POTTER)

It was part of a series and I’m pretty sure his name was Charlie and the title was formatted like “[character name] and the [plot relevant object/event]”. I barely remember any of the plot, but I think his mom was either dead or missing, at one point he was hiding in a well with at least one other person from some sort of beast that had attacked the school and he might have been scared of mirrors? The magic school system was split into three tracks, one of which was plant magic i believe. It was kind of like Harry Potter bc the book started with the school year and ended with the summer holidays