Since we can't physically prove the existence of God, nor bring down fire from heaven to smite said unbelievers (humour!), our defence against all of the above is to have our facts straight in the first place.
Know what you believe. Know where it comes from. Know how it all fits together.
The more I study the bible, the more I see how well it all fits together, how it has a beautiful internal logic and consistency, in stark contrast to the contradictory nature often ascribed to it by atheists or theologians.
Remember that we don't just face challenges from atheists; there are sects passing themselves off as true Christians, and also Christian theologists who study the bible intensely, but don't actually believe in God (or whose faith is weak and intellectual, rather than deep and relational), and delight in casting doubt on its authenticity, telling you that "oh, this verse was added 200 years after the original passage was written", or that this or that translation of the bible (e.g. KJV or NIV) or a passage "is not faithful to the original Aramaic/Greek and hence can't be trusted.." or that "there are books of the bible not included in this version which ought to be" etc.
Now, any or all of these things may or may not be true, but to me, it's an irrelevancy; we have to remember what and Who we believe in, and choose the one in Whom we are going to put our trust.
Don't we believe that God is in control of everything? I believe that He has given us an amazing gift in His word, and that He is powerful enough (and loving enough!) to ensure that it will always be available in all its truth to those who seek it.
How can I justify this? Firstly, remember that reading the bible is NOT the same as reading any other book - God bequeathed us the gift of the Holy Spirit, and states clearly in the bible that the Holy Spirit will guide us in our reading, supernaturally enabling us to understand God's intended meanings, and even using it as a direct conduit to speak God's messages to us, so that we can be guided by the Holy Spirit to bring us understanding of what we read, to draw our attention to see what God wants to show us. To illuminate the plain text into the divine word of God. It is a 'mechanism' which overrides any small translational differences between different forms of the bible, or any 'missing books' giving us the confidence to trust fully in God's word.
Remember, we're talking about a God of divine power here; who spoke to His prophets by means as varied and unfeasible as carving words into rocks with fire, or in the braying of a donkey. As an example of my absolute confidence in this principle, I am quite convinced that even if some one found half a bible lying in a ditch, old or new testament or an incomplete mixture of both, that God could still lead that person through the Holy Spirit to faith in Christ and grow their faith accordingly afterwards.
Be aware that in developing countries where bibles have been banned, entire Christian communities have thrived, based on only a rudimentary knowledge of a few bible verses!
(Read "The Heavenly Man" by Brother Yun, an amazing book about God bringing revival and sustaining Christians in China over the last 30 years)
We follow a LIVING God, a RISEN Christ of unimaginable power and love! Are we really going to let dried up, cynical theologies and empty philosophies tell us that our God cannot control the Word that He gave us? That His grace is not sufficient for us all?
So, put your trust in the almighty and ever-faithful God, not in the arguments of man, however intellectually persuasive or scientifically sound.
I note that prior to becoming a Christian, I felt that Christianity was full of inconsistancies (e.g. God's love and the suffering in the world), and theological conflicts (e.g. the aforementioned ones about whether the bible can be regarded as the unadulterated truth and the Word of God).
But since I became a Christian, what I realised is that all these 'issues' are merely a result of trying to apply an atheistic logic to a religion which is based on the central theme of a living God who provides supernatural guidance and intercession to His followers, and has assured them that He is real and has an active interest in their lives and in pursuing a relationship with them, and that furthermore, His plans are good, and designed to help us grow into better people and into a better relationship with Him (of course, this is often a slow process, and dependent on our willingness to LET Him do so).
There's dozens of examples that could be given to discuss this issue, but let's take as an example the much scoffed-at principle of 'no sex before marriage'; most non-Christians I've spoken to have regarded this as an outmoded and ridiculously contrictive law; another example of religions trying to get people to suppress their natural desires or make them feel guilty for having them etc and taking all the fun out of life.
And, if you examine the principle from an atheistically logical perspective, it's easy to see why they would think in this way:
What if you marry the wrong person? What if the sex is rubbish? How will you know if you're truly compatible with them (i.e. in bed, as well as out) without trying it first?
And why deny yourself all the pleasure in the meantime?
And numerous other reasonable concerns and criticisms!
However, to state a brief and modified creed of what we believe as Christians:
God is a living God, who has a good plan for our lives, and is involved in ALL aspects of our daily lives, including relationships, sex, and marriage!
He has assured us that if we live according to the Spirit (i.e. supernaturally guided, strengthened and enabled to follow God's otherwise demanding requirements by the Holy Spirit) then, we will be guided into making the correct decisions in life, into choosing the right person (that God had already planned for us to meet and marry).
God knows us totally, even better than we know ourselves. For those whom God has planned to be married, you can be assured that He knows (even better than we do) what kind of person is truly going to make us happy and fulfilled.
Finally, God cares about sex lives as much as we do, and designed it to be fantastic and free; only between a husband and wife as opposed to with anyone we feel like (two great books on this are 'Girl Meets Boy' and 'Sex is not the problem; Lust is' by Joshua Harris).
I fully encourage skeptics to read the book in the bible called Song of Songs, which is basically an erotic love song, describing the beauty of the female form and the sexual acts between man and wife, but with holy passion and cautionary advice to wait until the time is right.
The bible makes it clear that sex and desire are totally Godly, natural and to be enjoyed and embraced, but, within the appropriate time and circumstance!
God's good plan (if you are walking in accordance with Him so that He can guide you into it) is not going to lead you into a marriage with a rubbish sex life, or at least one that can't become great through communication, prayer, experimentation and love!
Also consider the romantic joy of being able to truly give yourself to one person only, body and soul, and know that you both had the exclusive pleasure of sharing this level of intimacy with each other alone; it's quite a wedding gift!
And, in further demonstration that God's plans are "to prosper us and not to harm us", consider:
In an ideal world (the way God intends for it to be, and indeed the way it is prophesised that it WILL become - the bible does indeed discuss heaven, but states that we will live on a new Earth, will all death, disease, evil and sadness eliminated and God living among us - Eden restored) all people would be true Christians, living spiritually and receiving the full life that God intends for them.
If we followed God's will and plan, and no-one had sex outside of marriage:
No one would need to worry about being an inadequate lover. Size envy/concerns would pretty much disappear. Sexually transmitted diseases would not exist. So many of the sexual hang-ups and insecurities that people suffer from would not exist.
So, it's not all bad, right? Perhaps (gasp!) God actually knew what He was doing all along? :p