The Bible tells us, with regard to atheists, “But the natural man receiveth not the things of the Spirit of God: for they are foolishness unto him: neither can he know them, because they are spiritually discerned” (1 Corinthians 2:14). Unless one is born again, or saved, he or she is “dead in trespasses and sins” and not mentally or spiritually capable of knowing the truth (Ephesians 2:1). Expecting understanding would be like talking to a corpse and expecting a reply.
When confronted by an atheist, don’t waste your time unless you feel led by the Holy Spirit to respond. If that happens, the Holy Spirit will tell you what to say. Do not get suckered into a debate.