Questions about deities must fade away just like any other issue fades away after it's been dissolved.
Compartmentalization is the last refuge for religious beliefs for an educated person. Once compartmentalization is outlawed there is no defense left. The religious beliefs just have to face a confrontation of the rational part of the brain and then the religious beliefs will evaporate.
If somebody has internalized the sequences they must (at least):
If you habitually ask yourself "Why am I feeling this way?", "Am I rationalizing right now?", "Am I letting my ego get in the way of admitting I'm wrong?", "Did I just shift the goal post?", "Did I make the fundamental attribution error?", "Is this a cached thought?" and all those other questions you become very good at telling which feeling corresponds to which of those cognitive mistakes.
So, let's assume that for these reasons the theist at least comes to this point where he realizes his earlier reasoning was unsound and decides to honestly re-evaluate his position.
A typical educated person who likes a belief he will continue to believe it until he's proven wrong (he's a reasonable person after all). If he doesn't like a belief he will reject it until the evidence is so overwhelming he has no choice but to accept it (he's open minded after all!). This is a double standard where the things you believe are dominated by whichever information enters your brain first.
The next step is to realize that religious beliefs are essentially just an exercise in privileging the hypothesis. If you take a step back and look at the data and try to go from there to the best hypothesis that conforms to the data there's just no way you're going to arrive at Hinduism, Taoism, Christianity or any other form of spirituality. All those holy books contain thousands of claims each of significant Kolmogorov complexity. We're dealing with a prior of 2 ^ -100000 at the least. Only if you start out looking for evidence for a specific holy book you can end up with a "lot" of evidence and believe that it can't be coincidence and that therefore the claims in the holy book have merit. Start out with a thousand holy books and a thousand scientific theories on equal footing (zero evidence for each, prior based on Kolmogorov complexity) and then look at all relevant things we know about the world. There's no way a holy book is going to end up as the best explanation because holy books are just really bad at making explanations that lead to predictions that can be tested. A holy book has to make more and better accurate predictions than the equivalent scientific theories (to compensate for the unlikely prior) to come out on top after all evidence has been examined.
I don't think it's possible at all to internalize the sequences and still believe in a deity. I consider this almost a tautology because the sequences are basically about good thinking and about applying that good thinking in all domains of life. Religious thinking directly rejects the concept of rationality about religious topics. So if you decide to be rational in all things (not cold and unemotional; just rational) then religion just has to go.
In an Open Thread comment beriukay mentioned that he's reading C.S. Lewis' Mere Christianity. I've been reading it too, for interesting reasons.
In my case it so happened that I started discussing faith with a long-time online friend whose spiritual views I didn't yet know, and he turned out to be a Christian with a high regard for the Bible, who also has an interest in science. As our discussion turned to our readings on spirituality, I acknowledged (I think it was me) that I probably spent more time on books that reinforce my point of view than on books that challenge it, perhaps a case of confirmation bias. (I've been exposed to many poor arguments for Christianity, and dismissed them; but possibly that was largely a function of having started out with that bottom line already written and picking arguments I wouldn't have much trouble refuting.)
In the spirit of experiment we agreed to a "trade" - he would read (thoughtfully and with an open mind) a book of my choosing on reasons to doubt faith, and I'd do the same with a book he chose on Christianity.
So the idea here is to pick a book that's the "best argument from the other side" (as in quote 3 here).
I recommended The God Delusion - I'm not sure if that's the best choice given the above intent, but it's what came to mind on the spot.
Would you make a different choice? If so, what?