Atheism, presupposition and religous prejudice

I was myself raised an atheist. In some ways this could be a disadvantage, as it makes my relationship with God maybe a bit less natural and relaxed than it would be if I had been raised in a religous tradition. On the other hand, I feel it is also an advantage to me in my philosophical labours, as it enables me to take a fresh look at the nature of the devine, perhaps making me somewhat less prejudiced than I would have otherwise been.
A note on this before I go on. Most atheists see themselves as religiously neutral, but this is in fact a misconception. My country is predominantly atheist, but it is an atheism firmly rooted in a culture and an environment heavily influenced by protestant christianity. That is why "Protestant atheist" would be a more fitting label on my nonbelieving countrymen than simply "atheist". I know many Indian atheists see themselves in this way, as Hindu atheists. It is only because of the tragic war between atheists and christians in the west that our atheists are unable to extend the same generosity.
I think many atheists (including my earlier self) fail to see how much their thinking relies on ideas that were concieved in a religious context. The humanistic morality is firmly based in the teachings of Christ, and could not have existed without them. This makes it somewhat of a contradiction when atheists accuse religion of doing nothing but cause war and trouble. Indeed, the very idea that war is wrong stems from the same phenomenon they are critizing for causing it.
Now, to the point. There are a number of presuppositions behind my philosophy, not the least of which is the existence of God. These presuppositions are based on faith, and would be hard to make a good argument for, though I will try, if challenged. Anyway, apart from these presuppositions, I try to be as logical, analytical and objective as possible. The whole goal of this blog is to present a complete and logically consistent philosophical system based on a few basic assumptions, in keeping with classical philosophical thinking.
The main problem with this is that my own philosophy will also say that such a thing is impossible. Human logic is a limited faculty, and can never claim to completely describe the whole of reality, as I am trying to do on this blog. This is actually scientifically proven by Quantum mechanics. On the smallest level, nature acts in a way that is entirely incomprehensible to our logical mind. It can still be described mathematically though, and mathematics are concieved by human logic, but it seems impossible to base philosphy on mathematics!
So, admitting that what I am attempting to do is impossible, I still attempt to do it. This is because I see no other way of doing it. Even though I can not hope to give a complete description of God and the workings of the universe, I can make a description that is as complete as possible, which is the next best thing. One of my favorite thinkers, the scholar, critic and philosopher Friedrich Schlegel, critized the enlightenment philosophers on these grounds, suggesting that the only way to publish valid philosophy was in the form of fragments - short pieces that all held, and admitted to hold, only a fraction of the truth.
I agree with Schlegel, but why should a fragment be small? This blog is an attempt to create a very large and thorough fragment, which in my opinion would be even better than a small one. I cannot hope to completely unravel the mysteries of the universe, but I can try to completely unravel them as seen from one angle. Together, a host of such angles would come closer to the ultimate goal.