One common error I see people make is that "God does not believe in atheists". The idea, in its essence, is that God has made His existence so clear, and even made it a basic instinct, that everyone knows He exists, and atheists are all 100% lying.
Scripture, however, tells us a different story. The phrase "never attribute to malice what you can attribute to stupidity" fits in very nicely with the Bible, because it does actually tell us that, as foolish as it is to do so, you absolutely can say in your heart that there is no God. Scripture even tells us that Christianity is foolish to those who are perishing, and that those who reject God can even be given over to their own strong delusions.
Make no mistake: Even the most sincere atheism is deliberate. God has made His existence so evident that denying it takes effort. If an atheist does not know there is a God, it's not because this is a reasonable position that one can be easily deceived into taking, but because they want to be deceived. Nevertheless, though it is a deliberate self deception, it is deception nonetheless. It is entirely possible for an atheist not to believe in God, and so I believe it is actually harmful to tell them otherwise. If you tell someone who knows they don't believe in God "you believe in God", they have more evidence to support their self delusion. Let us instead seek to guide them out of that delusion, taking the beliefs they do have, and show them why only God can justify them. From there, let us show them the power of the cross for salvation.