It is my strong opinion that you need to stop this relationship now. It will be a better witness to being a Christian if you let him know that God is more important than a relationship with an atheist. It may hurt him, it may mean it is over.
But dating is a preparation for marriage. If you don't stop the relationship now, you may end up marrying an atheist. Then what will happen to your children? You may have to spend your whole life going to church alone, praying for your husband to get saved. Instead, allow God to be in control.
I will pray for your boyfriend, because I don't like to see anyone walk away from God. But I am also praying for you, that you will walk away from a futile situation.
Your boyfriend may just see the real substance of your faith, and come back to Christ. But if you stick with him, he may never realize that serving God comes first. And neither will you.
Dating someone who is not a Christian (or so he is now saying) I called "missionary dating". It is not a good thing to do. Better to be a friend, and pray him back to God. Or trust God for the right man, and Christian to come into your life, so you can live a life equally yoked to a man who loves Jesus too.