Secondary school is a long way off so I would focus on what you prefer now, if you are Catholic and feel strongly about your children going to a religious school then I would go down that route.
Also, if you are religious you can do the Holy communion, confirmation on your own in your local church and then apply to Catholic secondary schools that way either. We are a catholic family with kids going to a non-Catholic school but I do plan on doing the church bit on our own time.
I wouldn't underestimate having to get a bus to and from school everyday, definitely not something I would choose to do unless I felt very strongly.