The first question I have is: Do your parents accept your religion, or do they think it's a "silly phase" or do they just stomp all over your beliefs? They seem to be of either the second or last following, so that's how I'll respond.
Eek... Either way, this is going to be rough, for both you and your child. The fact that your Christian parents have legal custody of him, (and therefore can choose to "make" him Christian since you're the biological parent but not the legal one... I knew I was Pagan at a young age, but my parents forced me to recieve all the Sacraments: Communion, Confirmation, etc, even though I consciously knew I wasn't Christian. So even if he doesn't want it, you son *might* be subject to going through things he doesn't want) and the fact that you're all living together is a big hamper on this.
I really, really, hate to the the pessimist, but even if you do attempt to teach him about tolerence, he'll be pretty much screwed because in Christian school, you'll be the "weird" parent, and he might be ostracised for it, perhaps even become ashamed that you don't fit into the mold that the other families fit in. Even if you both are very strong people, the peer pressure will come crashing through eventually... especially since he's getting mixed signals from both your parents and the school, and it'll be intermingled with his love for you. He won't know WHAT to do.
I went to a Christian elementary school and partly through middle school, and I'll tell you from experience that it'll either lead him to HATE Christianity up until his high school/college years, or it will make him into a good little Christian, intolerence and all.
I really wish you the best of luck on this, though.