Styley, that's a real dilemma. Once your little boy goes to school, religion is going to be very much on the agenda, so if you tell him God doesn't exist, it's going to be pretty confusing for him. He's only a baby, after all. Does he HAVE to go to a Catholic school? Can't you and your lady compromise and send him to an ordinary state school?
You're right. Religion shouldn't have such an influence in our lives, but it does, and it turns us all into hypocrites occasionally. I presume your partner is a devout Catholic? If she really wants a Catholic church ceremony, then I suppose you will have to go along with it, but just remember that the promises you give from your heart will be to her and her alone. Even though what you will be obliged to say in relation to God, will go against the grain, for the sake of harmony, you can probably cope with that. It's not ideal, I know, but what choice do you have? I would be more concerned about the Catholic school's influence upon your little boy, and the confusion that conflicting opinions are likely to cause him.