I think atheists and Christians do philosophy with different epistemological centers. What I mean by this latter phrase is this: an epistemological center is a cluster of beliefs, convictions, commitments, etc., which form a sort of critical basis from which proceeds the rest of a person's thought on some matter or other (or perhaps all matters whatsoever). For Christians, their epistemological center will be a commitment to upholding the testimony and tradition of Christian church regarding God, humanity, salvation, Jesus Christ, the eschaton, etc. -- the sorts of things you recite in the Apostle's Creed and the Nicene Creed.
Atheists do philosophy from a different epistemological center, and oftentimes I think they fail to understand that Christians do have a different epistemological center than atheists. This failure in understanding leads to a lot of misunderstandings and infelicities in argumentation.
For instance, in response to the skeptical theist objection to the evidential argument from evil, the atheist rejoins that such skepticism actually undoes the possibility of morality altogether. If God can be morally permitted in allowing grave evils such as the Holocaust, serial rape, etc., then maybe we are justified in failing to obstruct or prevent such things from occurring. Beyond the problem of putting God on equal footing with human moral agents, this line of response is abortive for another reason: it presumes that both the atheist and the Christian objector are responding to the problem of evil from the same perspective, from the same epistemological center. But this is not the case at all.
The Christian offers a skeptical theistic objection from her perspective as a Christian, which perspective already presupposes that she has adequate grounding for her moral convictions and practices in the teachings of Jesus Christ as passed down by the tradition of the apostles and the church at large. The Christian qua Christian doesn't approach the problem of evil from the same "neutral," uncommitted vantage point that the atheist does.
Rather the Christian qua Christian does philosophy from a prior commitment made to Jesus Christ and his church. The Christian takes herself to have had an encounter with God in Jesus Christ, an encounter which moved her to commit herself to him for life in response to a great, salutary act of mercy and benevolence accomplished in the cross and resurrection. She orients the rest of her life around this commitment, including her philosophizing, and so she doesn't approach the issues in the same way the atheist does.
Perhaps the atheist will rejoin that the Christian was irrational to do all that, that she lacked adequate evidence to make that kind of commitment. Unfortunately this line of response begs the question big time, because typically the Christian will not share the atheist's conception of what rationality, evidence, etc., amount to.
In any case, a nice tu quoque can be made to the atheist as well. She has numerous -- numerous -- starting points and background assumptions from which she began without adequate evidence. Her assumption of the existence of the external world, for instance: this is something presupposed by her arguing from evil for the nonexistence of God, but when has she ever justified this belief for herself by recourse to the evidence? No amount of evidence could justify this belief if her demands for rationality are strict enough, and even if she did bring forth evidence, this would almost certainly be a post hoc rationalization of her belief in the external world. No one believes in the external world because of some great argument or an evaluation of the evidence; it's something we start with, so to speak, though we may try to justify it later. But if she loosens her standards for rationality, then it's not obvious the Christian couldn't be perfectly rational in having made the Christian (moral, epistemological, existential, metaphysical) commitment.
There is also a further point to be made. It just might be that a failure to behave strictly "rationally" at some points in time are not all ultimately objectionable in this grave way, as if "irrationality" were the gravest and most indecent of crimes. Especially if the Christian is right about her beliefs, her irrationality -- just as any number of other sins -- may be forgiven her. The rationality of her belief, for this reason, is less interesting and consuming a topic than the truth of it. She, on the other hand, offers an invitation to the unbeliever to faith, to participation in the Christian community as a means by which the atheist may come to see things previously unknown.