I still don't quite get it - you're making it seem like both particles are interchangeable, but at the same time not. So, just to make things clearer on a concrete example: please explain the difference between 子供が 遊んでいる and 子供は 遊んでいる. I am not a native, or anything even close, so if 遊んでいる is not in the right clause, please ignore it and concentrate on the が vs は part.