I haven't gone through and read the posts that preceed mine, but it seems that many debates over the existence of God/ influence of God over reality presuppose an "either/or" mentality.
There is an atheist by the name of Richard Dawkins who discussed in a book his concept of a "god of the gaps." His idea is that people use God as an attempt as an explanation for the workings of any misunderstood natural phenomenon, only to abandon this once a naturalistic explanation has been found. (I am not an atheist anymore, but I do like to hear all sides of any argument that interests me.)
Assuming that God does exist, is theistic (rather than deistic), and is truly omnipotent and omniscient, then the only analogy that I can think of to compare this to is virtual reality.
Let's say I were to step into a computer world (like the Matrix or a video game or whatever). I am walking down the street, and to my side I see a red ball. I kick it and it rolls a few feet ahead of me, slowly coming to a stop.
Now, everything in that situation can be explained though physics. But does it mean that the massive supercomputer running the virtual reality world had no part to play, or that it is a contradiction to say that both the laws of physics and the supercomputer make it move? On an immediate, superficial level, you could argue that it must be that the supercomputer had no part to play. But would it really be a contradiction to say that, on a sublime level, it was all by the invisible hand of that supercomputer?