Yeah, go with your comfort level. Most of the time I was at school I was presenting female, so I tended to use the gender-neutral bathrooms when possible.
Been in the mens a handful of times, though. Hasn't generally been too much of a problem, especially since they tend to be less crowded.
(the one time it was a problem was the day I was wearing a dress to school and wandered into a mens room, thoroughly confusing some poor fellow)