You shouldn't have a problem with being non-religious in a Catholic school, as long as the school is not overly strict. I speak from experience...Since 1st grade I've always been to Catholic Schools, when I was younger I used to believe in God but I was never excessively religious and it was fine. Then, at about age 16 or 17, suddenly a lot of people start to "lose their faith", so discussions in religion class became rather heated debates. Some day I realized I was on the side of the non-believers, too... Most teachers are okay with it, my religion teacher was actually pretty glad that me and my friend were of the non-Catholic/atheist opinion because it added some spice to discussions.
So speak your mind when you feel you need to do it, maybe don't just shout it out at every occasion... a peaceful coexistence should be possible.
And are you sure that in that school people wear school uniforms? In my school we're allowed to wear anything we like (and actually, when I wear a schoolgirl-type short skirt people are somewhere in between amazed and shocked).