As I mentioned somewhere in another thread, I have found being grounded in a solid community with wise leadership from a priest or pastor to be indispensable.

I don't think there is one best way. It will depend on what is in doubt and on the doubtor.

What is the most central doubt for you?

I also have come to think that most doubt arises from sources other than philosophical reflection (which is distinct from saying that it is non-rational).  I think this is true whatever side of an issue you take.  More people begin to seriously doubt theism because they go through a crisis in their lives than because they read a book by JL Mackie; but also more atheists start to wonder whether there may be a God after all because they have a religious experience rather than reading one of Fesser's books.  (The converse, however, does happen too, of course.)

I bring this up because I think philosophically minded people frequently have a difficult time being honest with themselves about this element of their psychology.  They find themselves struggling with doubt so they double-down on reading arguments.  Really, the issue is that their daughter was just diagnosed with cancer or they are frustrated for failing to overcome a protracted habit of sin or, for the atheist, a longing to be loved begins to be met by a Christian community or a good priest.  I think being honest about these diverse motivations for why we think what we think can only make us better philosophers.