Not sure if this will be at all helpful, but this is what the OP brought to mind.
As PPs have said, Scripture was intended to explain the most significant things about God and His relationship with humankind. Yes, the universe was brought into existence by God. Exactly how and when He did this is not explained, except sometimes metaphorically; we would not be able to understand a description of how God created time, space, and matter even if one could be written. More to the point, how would that information help us?
The creation of the universe was a miracle, in the sense that we cannot understand how it was done, and it was accomplished outside the set of natural laws we observe every day. It makes very little sense to say, "How could God bring the whole universe out of nothing? Nobody can do that!" It is certainly true: logically the universe should not exist, wherever it came from. But it does exist. The same applies to life on earth, which was either created out of nothing, or rose spontaneously out of non-living matter. Both are unlikely in the extreme. Accept that our being here is impossibly weird, and move on.
The same applies to other miracles. They are "miracles" because they occur outside the "rules" of nature. In the ordinary course of things, people do not come back to life after decomposing in the tomb several days, or conceive a baby without having sex, or ignore gravity. This can only be done by someone who is operating outside the rules, who invented the rules in the first place, and who is outside, and beyond, the game entirely. No matter what philosophy you apply to the natural universe, religious or scientific, you have to eventually arrive at something/someone which is outside/beyond that universe. When you get to that, any discussion about natural law becomes absurd.
We often hear that Christians bend and twist the Bible (or other information) to conform to predetermined ideas, and frankly, it is very often true. What I think is equally true is that science often does the same. Science is sometimes presented as the opposite of religious faith, something totally rational, something that has no agenda, but just looks objectively at the evidence. In reality, I think science has its own preconceived notions. It has limitations. In the end, when we all find out the true origins of the universe and everything living in it, I assume we will all be surprised, believers and scientists alike. I take the view that the vast majority of what we "know" about the material world is wrong, but fortunately our lives and souls do not depend on accurate data. If that were true, mathematicians would be the holiest people on earth, and shepherds would have no chance of being saved.
: While there may be some ignorant, silly people who are Christians, that doesn't meant that Christianity prompted their ignorance. 
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