A few days ago I thought I had an idea that was worth trying out on a blog. Let's see if I can recreate it now.
Descartes divides created substance into two kinds (matter and mind), with matter a deterministic, mechanical, mortal realm, a bit like Plato's world of becoming. Minds are then 'outside' this realm, although they can interact with it and each person's mind is spread throughout her body. They have free will and are immortal. Free will allows for moral responsibility and immortality allows for punishment and reward after death. So traditional religious ideas still have a place despite the modern, scientific conception of the physical world. This metaphysical dualism is defended using the method of doubt, an epistemologically-informed methodology.
Kant divides everything that exists into phenomena (or things as they appear) and noumena (or things in themselves), but whether this distinction is metaphysical, epistemological, or neither is hard to say. At times he seems to be talking about the same things conceived in different ways (as we know them and as they just are), but at times he seems to be talking about different kinds of things: our phenomenal selves are mortal and lack free will, our noumenal selves (we ought to believe) are otherwise. God is not a phenomenon but might belong to the realm of the noumenal. We can only know about things as our minds conceive of them, and so there is a limit to reason, which means there is room for faith. This metaphysical/epistemological/whatever dualism is defended using the transcendental or critical method, which is concerned with the conditions of possible experience. So this is a kind of logical or conceptual method.
So far you are probably a) completely lost (if you don't know any history of philosophy), b) yawning uncontrollably (if you do), or c) outraged at some crass blunder I've made in the above. But I'll assume you're somewhere around b and try to get more interesting.
Kant's hard-to-pin-down position can be regarded as a transitional point between Descartes and Wittgenstein. The method that Wittgenstein describes in Tractatus 6.53 could be compared with Descartes's method of doubt. Rather than discard whatever can be doubted, though, we discard whatever has been given no meaning, i.e. anything metaphysical. The mysterious realm of the noumenal has become the realm of nonsense. But since ethics, aesthetics, etc. belong to this realm, Wittgenstein is often regarded as a mystic rather than as a Dawkinsy positivist.
The later Wittgenstein is also regarded by some (Lyotard, as I remember his work, is close to this position) as defending faith by confining it to one or more language-games that have different rules than other games, such as science and rational debate.
All of these dualisms (and the fideist pluralism) have their problems. Cartesian dualism is based on bad arguments and involves violation of the laws of physics for something outside the physical world to change the course of events within the physical world (i.e. non-physical minds exercising free will by changing the direction of moving matter). Kant's theory involves a lot of necessarily puzzling references to 'things' beyond the mind's ability to comprehend and also seems a lot like wishful thinking: we cannot know whether God, free will, or immortality exist, but we'd better have faith that they do. Tractarian mysticism seems no better than this and might be even worse: I know my beliefs don't make any sense (or should that be "sense"?), but I'm sticking with them anyway. And the fideist language-game theory seems like an annoying cheat: what right does anyone have to fence religion off from rational criticism? And, from a religious point of view, why should religion need a fence around it?
The truly Wittgensteinian position, it seems to me, refuses to erect any such fence. Nor does it stipulate what we can and cannot do with our language. It is ours, after all, and we can change the rules if we want to. So even if "the" language-game of religion is distinct from that of science, this could change. So philosophy cannot produce textbooks or well-established hypotheses or theses. It must be flexible. It must be conceptual, so it must be linguistic. Not as a scientific study of language, but as a linguistic study of language. A study from within. And that means it must be conducted as a conversation. Which means that this post itself, especially all the imperatives in this paragraph, is highly suspect.
But it is only a blog post, after all, which is perhaps as much as any philosophical remark should aim to be.