I lived in Berkeley, California, for 5 years, right downtown, a block from City Hall. During that time on multiple occasions I spoke on creationism to skeptical atheist groups and to various groups on the U.C. Berkeley campus.
I would say firstly to begin witnessing to them with prayer and love. The atheists like to see themselves as "smart" in dispensing with the old superstitions and religions of the past. One needs to appeal to their intellect while praying for their souls. They are NOT our enemies. (Actually, unlike many modern Christians, I actually like speaking with atheists. It can be invigorating to discuss presuppositions and truth seeking with a true atheist amidst the cacophonous philosophies in the world today.) How do we determine "truth"? What is real? Rene Descartes said, "I think therefore I am." (Or my variant: "I think I think, therefore I think I am.) ... Okay, back to atheists and devout skeptics.
They are smart humans, but with deceived souls. Even a smart person can be deceived, in fact it is pride (not intelligence) that can be the main problem. Pride goes before a fall (Proverbs 16:18). They've mentally dispensed with notion of the Bible as revealed truth. Some of them came from religious homes - but they saw hypocricy or abuse that drove them away spiritually. Maybe their father was a tyrant with enforced Bible thumping (but no love). Maybe the pastor or rabbi ran off with a secretary. Or there was an abusive priest in their background. "If that's religion - they can keep it!"
Jesus did not stand with the religious leaders of His day. And we shouldn't either. Too many hypocrites are among those who are the "most successful." But logically speaking, the fact of counterfeits out there does not negate the value of the real ones (whether in currencies or in persons) when we find them. Jesus could have chosen 12 well-trained rabbis of the day as disciples. Note that He did not choose a single trained theologian. He surrounded Himself with 12 average but teachable guys with mostly blue-collar backgrounds. But as happens with every belief system, it becomes institutionalized. For both Judaism and later Christianity the leaders soon began to co-mingle their embellished traditions with the Word of God, i.e. the Bible. That was as true then - as it is today! In fact, many times Jesus Christ answered the Pharisees and other religious leaders with "For it is written..." and "Have you not read ...?"
We do not want to "defend religion" when trying to reason with (and pray for) an atheist friend.
Some atheists, though very intelligent, have many fears. Their beliefs of (or understanding about) the universe leave them oh so vulnerable. Fellow believer, imagine someone thinking that they need to be "strong" by NOT reaching out to "G-d" in prayer! (Of course, it actually takes more strength to admit weakness, than to "stand strong" and deny our human frailties.) When I have spoken to atheist groups I write a prayer on the board: "Creator, if you are there and if you can hear me, please help me." Some will laugh, but I want them to consider later praying this, when alone. Be strong enough to admit weakness and need.
Me vs. the universe and its God. Okay, so someone crosses his or her arms, "You can't prove God exists to me! So there." I would answer, "Yeah, not anymore!" The Bible says that God resists the proud but gives grace to the humble. If someone wants to strongly deny and deny, that is their right. But it closes the door of communication with God, whom we must approach humbly. So let's take a different approach: Trillions of galaxies and stars, quasars, the expanse of deep space. The pale blue dot, with one micro-pixel on its surface that is - me. The beauty of the wind going across a field, or the ocean waves at sunset. Bees and pollen. Fragile butterflies. Ummm ... the God of such a universe answers to - (micro-pixel) me? I don't think so! Logically, we need God a lot more than he needs us. Get used to the idea. We are on a planet that is owned. If a farmer decides to till under an entire crop that is his right. Or maybe he waters one field more than another. It is his land. When someone claims that children dying of malnutrition is "proof that there is not a loving God out there" they are presuming a human-centric (pre-Galileo; universe-revolves-around-us) attitude. The Bible does not teach that. We are worth more than a sparrow that falls from the sky, (Matthew 10:29-31), but it is not all about us. Also see Job, chapters 1 & 2, or C.S. Lewis' book, The Problem of Pain.
In love, let us reason with and pray for them. Jesus said (Matthew 11:25), "At that time Jesus answered and said, I thank thee, O Father, Lord of heaven and earth, because thou hast hid these things from the wise and prudent, and hast revealed them unto babes."
It is sometimes easier for us less sophisticated thinkers to accept Christ than for someone with a very high IQ, or beauty, or lots of money, or impressive powers of persuasion. They miss the most important part of life - our relationship with our Maker. Encourage them to read the New Testament, and to pray. Reach out. Not with pride, not with accusations against God. Instead ask, seek, and knock. God is right there. But He does not have to prove Himself to you or to me.
Take a look at Dr. Hovind's Debate series: http://shopping.drdino.com/category-exec/category_id/36/nm/Debate
(But Dr. Hovind too, like all humans, was susceptible to deception. He is a brilliant creation speaker. I highly recommend his creation teachings. But for many years he fought against the government on financial and church-related issues. He eventually lost in federal court and is in a federal prison, serving a 10 year prison term. I mention this because almost all skeptics seem to have learned this, but many Christians over 3 years later now, still do not know this. Yes, this would appear to discredit his teachings. But even if one has error in one area, perhaps we could still learn from them in another, right? I know many computer "nerds" who have made foolish financial investments or romantic decisions, but they remain brilliant programmers. Or there are some politicians who have had sex scandals but can exercise good political judgment, correct? One could learn good biology from an atheistic biology professor, right? Go around his atheistic beliefs, concentrating on the biology. -Well, perhaps similarly just consider Dr. Hovind's creation teaching on its merits. He has done over 100 debates with evolution-teaching professors and learned skeptics. 20 of these are on DVDs, per the link above.)
Would your atheistic friend be willing to read C.S. Lewis' book: Mere Christianity? Or another excellent place to start with the fourth book of the New Testament: John (also called: The Gospel of John).
I mentioned Berkeley, and the atheists there. If it is helpful, here
is a link to one of my 28 minute videos, dealing with God's existence:
(See video #1.)