Just because something is beyond our comprehension doesn't mean it is impossible.
For instance, as I understand it, no-one knows why aspirin works, but it does.
I don't understand quantum physics, but that doesn't mean quantum physics doesn't exist.
Just because I can't get my head around the concept of God existing, doesn't mean that he is not real.
Of course, just because I can't fully understand it doesn't mean it is true... otherwise all kinds of crazy stuff would exist.
So how do we tell the difference between something you can't understand that is true and something you can't understand that is false. If you can't understand either, how do you evaluate them?
I guess a first step is to evaluate whether the conclusions formed by assuming it is true actually hold in reality. If they don't hold then it means your assumption was wrong - either in it's basic assumption or in it's expression... or I guess in the logic you built on top of it.
So how does this apply to God? I think I'll write another on that...