Following is both a reproduction of an atheist’s set of questions to Christians (in brown) and my responses (in green).  It came from challenging-religion.blogspot.com.  I have permission from the atheist to reproduce his questions so that I could respond to them here.  His questions are illustrative of the lack of understanding by atheists of both logic and Christian theology.  My recommendation is that atheists study both if they want to be a serious intellectual challenge to the Christian faith.

1. Does God have free will?
   1. If you say yes, can He choose to do evil?  No, God cannot choose to do evil.  God cannot act in a manner that is contradictory to his own nature.  His nature is holy, and he is not capable of doing that which is contrary to his own nature, namely, sin and/or evil.  However, evil would need to be defined here as well.  Within Christianity, evil has at least two different distinctions. There is ontological evil which would be, for example, the person of Satan who is evil by nature. There would also be what’s called natural evil which is referenced in Isaiah 45:7.  The latter is different than the former because the latter deals with disasters where the former deals with an evil individual whose will and purposes are to do harm without just cause.
      Furthermore, an atheist would have no objective grounds by which evil could be determined and a standard established.  Without a standard, nothing more than opinions can be offered as to what is good or bad, right or wrong, and evil or not evil.  There may be things that are unpleasant or not preferred, but this does not constitute evil in the ontological sense. 
   2. If you say no, why not?  The answer has already been explained.  God cannot act in a manner contrary to his own nature.  Evil is contrary to his holiness, so God cannot choose to do evil.
   3. If you say yes, then doesn’t that mean that your God’s actions are questionable?  Since God cannot do evil, his actions are not questionable.
   4. If you say yes, then can he have a state of uncertainty? (See the free will argument against God’s existence).  See above.
2. When having discussions like this, it is first necessary to define terms.  Free will is the ability to make choices.  However, our choices can only be made within the confines of a person’s nature.  For example, though I am free to conceive of many things I might want to accomplish, I’m not always able to accomplish what I desire.  I could conceive of the idea of flapping my arms to fly to the moon, but I’m not able to do it.  Likewise, I cannot conceive of something that I cannot conceive of.  If I cannot conceive of something, I cannot make a free will choice to want it, accept it, reject it, or whatever.  So, free will does not mean that a person has the ability to do anything.  Instead, it is the ability to make choices within the constraints of our nature and not in a manner that contradicts it. 
3. What crime deserves an eternity of punishment?  Any crime against an infinitely holy God deserves an eternity of punishment.  It is not an issue of any particular crime that deserves an eternal punishment but who the crime is against.  Let me illustrate.  If a man were to slap another man in the face, the result might be an argument or even a fistfight.  However, if that same man were to slap the President of the United States in the face, the result would be quite different.  The person would go to jail and face felony charges.  So, why does the exact same act get such different results?  The answer simple. It is not the act that deserves a higher punishment.  Instead, the different result is determined by who it is against.  So, if we move up the chain of command to the infinite God of the universe, when we break his law, there is an eternal consequence because of who the crime (sin such as lying, etc.) is against.
4. What does it mean to you when you say that Jesus, God, and the Holy Spirit are one God?  This is not an issue of “what does it mean to me.”  The question is what is the biblical doctrine of God?  The answer is simple.  The Bible teaches that there is only one God in all existence (Isaiah 43:10; 44:6, 8; 45:5).  Furthermore, the Bible teaches that God is comprised of the Father, the Son, and the Holy Spirit who are each called God, who each have a will, each recognize the existence of others, and even speak to each other.  This is not illogical, but it is paradoxical.  So, the biblical doctrine of God is known as the Trinity.  This is the teaching that there is only one God in all existence who is comprised of the person of the Father, the person of the Son, and the person of the Holy Spirit.  For more information see (What is the Trinity?).
5. For Christians who pray to Jesus in hope he will intercede with God, does this make sense if Jesus and God are one and the same?  This question reveals a lack of understanding of the doctrine of the Trinity.  When we say that Jesus and God are one and the same, clarification is necessary.  In Christian theology, there is what is called the ontological Trinity and the economic Trinity.  The ontological Trinity states that each member of the Godhead (Father, Son, and Holy Spirit) share the same divine nature.  The economic Trinity states that each of them has a different role.  For example, the Father elects, the Son redeems, and the Holy Spirit convicts of sin.  The Father sent the Son, but the Son did not send the Father.  The Holy Spirit is sent, but did not send the Son.  So they are the same in their divine nature, but they are not the same in that they are distinct persons and exhibit different roles.
       So, Jesus the Son is praying to God the Father.  Also, Jesus is both divine and human (hypostatic union).  As man, he is able to die for people, and as divine in nature, he is able to appease the person of God the Father.
6. If human evils must be allowed so that we can have free will, then why did God also create natural evils? (i.e., floods, disease, etc)  This question is insufficient.  It begs the question by saying that human evils must be allowed in order to have free will.  God, who cannot commit evil, has free will. So the idea that free will necessitates allowing evil demonstrates an insufficient understanding of the concept of free will. 
7. Is your interpretation of the Bible correct?  This question is insufficient.  Does the person mean the entire Bible, every single verse, major concepts, or what?  There are certain doctrines within Christianity that are not debatable (essentials), but there are other ones that are debatable.  Romans 14:1-12 tells us that there are debatable issues.  So even within the Bible, we are told that there are things that are debatable.  To ask if a particular person’s interpretation of the Bible is correct, how is one to answer that considering that the Bible says there are debatable issues?
   1. If so, how do you know?  A person’s interpretation of Scripture is correct only in so far as is consistent with what the Bible says.
   2. If not, why do you follow it?  Are you saying that Christians will knowingly follow an interpretation of Scripture they believe to be wrong?  I hope that is not what you’re implying.  If so, it is yet another demonstration that the question has not been properly thought through and/or expressed.
8. Why are there over 30,000 Christian denominations all claiming to be the “true Christians”? Which one should I follow and why?  Where is the documentation that demonstrates there are 30,000 denominations?  Please define what a denomination is so we might check it against any documentation.
   Christian denominations differ on debatable issues but not on the essentials.  Let me illustrate.  Let’s say there are 12 football teams in a division.  They have different representative colors and different strategies.  If someone were to ask which one is the “true football team” and which one should people follow, it would demonstrate a lack of understanding of what football really is.  It would be a wrong question to ask.  So, the initial question is another demonstration of a lack of understanding of Christian theology in the essentials, in the nonessentials, as well as what constitutes a denomination.  In addition, it does not provide any documentation to demonstrate that there are 30,000 so-called Christian denominations.
9. If God told you to rape your mother, would you do it?  This is an illogical question.  It is asking to answer based on an impossibility.  God would never ask anybody to commit such a sin.  It can’t happen and would not happen.  Therefore, it is an invalid question and demonstrates a serious lack of understanding of Christian theology . . .
   1. If not, then aren’t you conceding there are some commandments that qualify disobedience to God?  See above
10. Why are modern-day miracles less impressive than those in Biblical times?  Which modern-day miracles are you talking about, and by what standard would you judge something to be more or less impressive?  Also, which individual’s standards would be the ones by which you would determine what is more impressive or less impressive?  Without answering those questions, your question can’t be answered.
11. Do you believe in any miracles that are recorded outside the Bible?  Yes.
    1. If not, why not?  Not applicable.
    2. If so, then why should I believe the Biblical miracles?  Why would my believing that miracles occur that are not recorded in the Bible bring any doubt upon why I should believe the Bible?  This makes no sense.
12. Is predestination true? (original link to carm)– Yes, per Eph. 1:4-5.
    1. If yes, then what type of God will create humans to purposefully torture people in hell?  If God, the real God, creates people to go to hell; what is that to you? Does not the sovereign Lord have the right to do with his creation as he sees fit?  You may certainly not like it, but your liking it or not is irrelevant to the reality of its occurrence.  You have no standard, as an atheist, by which you can judge that such an action is right or wrong.  At best, all you have is your opinion.  Still, Prov. 14:6 and Rom. 9:22-23 answer your question.
    2. If yes, then do we truly have a say in our Salvation?  Predestination teaches that God foreordains whatsoever shall come to pass (Eph. 1:4-11).  In the context of Christians, he predestines the elect (those chosen) into salvation.  Furthermore, the question also fails to properly understand the doctrine of total depravity which states that a sinner is enslaved to his sin (Romans 6:14-20) and will only choose sinful things because he cannot perceive spiritual truths (1 Cor. 2:14).  Therefore, without predestination, none would go to heaven.  The “say” that we have is that we receive Christ (John 1:13).
    3. If yes, then what is the basis of God’s foreknowledge?  Where does this question come from? What do you mean by foreknowledge?  How does it relate to your question?  I strongly recommend that you explain terms when you introduce them.  This will avoid confusion.
13. Is there any amount of evidence that one can give that will cause you to leave Christianity?  Yes.
    1. If so, what is it?  Demonstrate that Christ did not rise from the dead.  All that would be necessary is to find an ancient tomb with sufficient archaeological evidence in it to substantiate that it was Jesus of the New Testament who was crucified and failed to rise from the dead.  In such a case, I would give up Christianity.
    2. If not, then don’t you have blind faith?  Blind faith is held by atheists.  They cannot demonstrate that God does not exist.  In spite of the dilemma of trying to prove a negative, they demonstrate great faith that their assumptions about God’s nonexistence (or lack thereof) properly represent reality.