IRL, you are supposed to use the pronoun for gender the person associates themselves with. It often works in manga discussions too.
When dealing with complicated manga situations, I recommend using the character's name or position in the story ("main character", usually) instead of pronouns, because there is no word to describe the situation MC found themselves in.
There are also specialized words that can be used in gender-complicated situations, such as "gynophilic" for people attracted to people who look female (because Ranma night be a girl or a boy depending on which water he's been doused recently, but he's only attracted to girls in either form, so descriptors like "heterosexual" or "homosexual" are not useful). But most of the time, you'll need a lengthy description, like "man trapped in a female body).
I hope it helps. Because I am more confused after writing all that.