Even though you’ve framed this discussion around the story of Noah’s Ark, I think you’re right to direct the conversation toward a more general question about how we ought to understand the bible. And the account of the Flood is a great backdrop against which to examine this issue.
It’s important to recognize that the controversy over Noah’s Flood needs to be placed in its correct context. There is a loud group of Christians (I’m thinking specifically of the Ken Ham types. Let’s call them the ‘Hamites’) who have dramatically overemphasized the importance of a particular interpretation of the Flood. The Hamites have argued very plainly that the truth of Christianity rises or falls on whether or not there was a worldwide flood. For the Hamites, believing in the worldwide flood is essential to Christianity. For example, the Answers in Genesis website had this to say:
God’s Word must be the final authority on all matters about which it speaks—not just the moral and spiritual matters, but also its teachings that bear on history, archaeology, and science.
What is at stake here is the authority of Scripture, the character of God, the doctrine of death, and the very foundation of the gospel. If the early chapters of Genesis are not true literal history, then faith in the rest of the Bible is undermined, including its teaching about salvation and morality. 
Let’s be plain and clear about this: Christianity can be true while the Hamites are wrong.
The first issue for Christians to consider is whether or not we ought to take to the Bible to be inerrant or not. If a Christian considers the Bible to not be inerrant, then there is no problem of the Flood to solve. The Flood is only myth; myth that perhaps has an important moral message, but a myth nonetheless. For this Christian, Genesis (and the rest of the OT for that matter) is just a collection of stories that have been redacted, edited, and evolved over time to fit the needs of a community. The story of the Flood was created to scratch some didactic “itch” that the Hebrews had.
However, if a Christian does hold to inerrancy, then the issue of Noah’s Flood does become something of an issue, and there are a number of facets to consider. The first issue is` what we mean when we say that the bible is “inerrant.” The doctrine of inerrancy is something that is often misunderstood by both Christians and atheists alike. Typically, the doctrine of inerrancy is distorted into something like this:
“The doctrine of inerrancy means that every word of the bible must be taken completely literally.”
But, this is most certainly not what the doctrine teaches. In fact, a doctrine of inerrancy like that will end up reflecting the interpreter more than the text. If we take the bible completely literally, we end up making all kinds of assumptions about the text that may or may not be justified. When we simply take a text “literally” we often ignore the intent of the author his place in contemporary culture. Consider this verse from Matthew:
He replied, “Because you have so little faith. I tell you the truth, if you have faith as small as a mustard seed, you can say to this mountain, ‘Move from here to there’ and it will move. Nothing will be impossible for you.” 
If we take this text literally, we end up saying that faith is something that has physical substance and can be measured in physical dimensions. If we had two mustard seeds of faith, imagine the sort of power we could wield! Perhaps one mustard seed of faith contains the same amount of energy as one hundred tons of dynamite!
The point is that quite often to read the bible literally is to misread it. An accurate interpretation the bible requires careful consideration of context and culture. We must strive to understand what the author intended and not be satisfied with what strikes us as being the “literal interpretation.”
Interpreting the bible is a much as science as it is an art – a discipline called hermeneutics. And some Christians are just bad at it.
Consider the quote above from the AIG website. The Hamites really go beyond assuming that Moses’ work should be taken literally, I think they are further assuming that Moses is writing history like a modern historian would. They think Moses is trying to give an objective, third person account. But, I think that when we consider the culture and means of communication contemporary to Moses, it’s more appropriate see Moses’ purpose as didactic and not the sterile recording of history. Moses is trying to tell us something about God and his relationship to mankind more than he is trying to give us empirical data.
This, of course, would not mean that the account of the Flood is not scientifically accurate. All it means is that we should not appeal to Genesis as we would a scientific textbook simply because it was not Moses’ intention to write a science book. If science informs us that something different than what a literal reading of Genesis would give us, then perhaps it is our impetration of Genesis that needs adjusting, not science.
Further, the Hamites begin with a bad hermeneutical principle: the book of Genesis must be literal history. But this is an assumption that is imposed on the text (something called “eisegesis”) and not derived from it. If as Christians we are committed to the doctrine of inerrancy, then we shouldn’t begin a study of Genesis as saying that it must be literal history. We should begin with a more conservative position: perhaps this text should be taken literally or perhaps not. We ought to begin by searching out the meaning the author intended to communicate in the text. And this is exactly the kind of principle that a good definition of inerrancy incorporates. Consider Erikson’s for example:
The Bible, when correctly interpreted in light of the level to which culture and the means of communication had developed at the time it was written, and in view of the purposes for which it was given, is fully truthful in all that it affirms.
So we can’t just interpret the bible with the broad principle of “it must be taken literally.” Instead, we need to get at the meaning the author intended. It may be the case that Moses did not intend all of Genesis to be read literally. And we need to further realize that if it turns out that we discover that the author of Genesis did intend for his writing to be taken literally and a literal reading turns about to be wholly irreconcilable with science, then the whole Christianity does not collapse in on itself like the Hamites imagine. We simply need to adjust what we believe about the bible. Perhaps it is inspired without being inerrant.
Because this is the case, the debate over Noah’s Flood belongs in a discussion between Christians. The veracity of the biblical account of the Flood is not really something that ought to interest atheists simply because whether or not there was a global flood does nothing to prove whether or not Christianity is true. The most ground a skeptic could gain is the ability to dismiss the Hamites – something they’ve already done anyway. Of course, atheists and skeptics should be welcome to criticize the Hamites or any other Christian belief, but the point is that if the Hamites are wrong about the Flood, it does nothing to prove that Christianity also is. This means that debate over Noah’s Flood and how it ought to be understood is an “in-house” debate between Christians.
As a side note, it’s worth pointing out that the basic argument against the flood is a geological one. And there is a prevailing assumption in geology called “uniformitarianism;” the belief that the world in the past operated by the same principles we see today. We take about 200 years of scientific observations and extrapolate that out to 6 billion years of earth history. Granted, this assumption has proved fairly reliable, but even recently, because of a commitment to uniformitarianism, scientists were reluctant to accept that craters were instanteously created by catastoprhic asteroid collisions and not formed slowly over millions of years by volcanoes. So perhaps lapse into fundamentalism is something that even scientists should be wary of.
So I think the end result is that we are allowed some flexibility with Moses’ account of the Flood. It may be the case that Moses is using exaggeration or overstatement to describe an event that really happened. Perhaps he’s referring to a local and not global flood. But we can also wait for more evidence to come in. Perhaps paradigms in science will shift. But if doesn’t, we should not be surprised or discard all of God’s revelation if it turns out a particular interpretation is incorrect.
For a great overview of the kinds of interpretive issues that need to be considered, I’d recommend reading through Nathaniel Claiborne’s blog series on Genesis
 The doctrine of inerrancy is a “sub” doctrine of the doctrine of inspiration. A Christian could hold that the bible is inspired but not inerrant. Indeed, many do. A Christian could further hold that the bible is not inspired, but they begin to seriously separate themselves from orthodoxy at this point.
 Erikson, Systematic Theology, 259.
 However, I don’t think we need to make that retreat just yet.
 Though I think we ought not pretend that only the field of geology poses a challenge to the idea that a universal flood happened roughly 10,000 years ago.
 National Geographic: Asteroids: Deadly Impact (Documentary).