How does John feel about Edward's atheism and what led to it? How do the novel's characters convey different views on salvation? What is your perspective on the fate of souls and worldly pain?

Quick answer:

1. Ames seems to accept his brother's atheism. 2. Edward leaves the church because he believes that it is not contributing to society. 3. Opinions on salvation vary among characters, but no one specifically states their opinion on it. 4. Answers to questions posed by John would depend on personal interpretation of humanity and the nature of pain in the world. Question 3: How do the novel's characters convey assorted possibilities about this topic?

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Ames's relationship with atheism is an accepting one. The father of Ames and Edward is very upset to hear of the latter's atheism: “There was rage and weeping in my mother’s kitchen and that my father was in the attic or the woodshed, in some hidden, quiet place, down on his knees wondering to the Lord what it was that was being asked of him. And there I was with Edward, trailing along after him” (27). However, although Ames sees the anger of his parents towards Edward's beliefs, he himself remains steadfast as a supporter of his brother. He admires his brother as intelligent and critical and does not dismiss his brother's atheism.
One of Edward's favourite writers is Feuerbach. Ames states: “I’m going to set aside the Feuerbach with the books I will ask your mother to be sure to save for you” (27). This signals his acceptance of his brother and the atheist writers he is interested in. He wants his son to explore atheism, and his own beliefs, regardless of the prominence of atheism in his life. Edward leaves the church due to an increased education and understanding—he feels that the church does not contribute to humanity and the poor. 
John is a Calvinist, which influences his feelings and behaviour. He does not feel that Edward's atheism condemns him to hell, because Edward knows everything in life and is therefore pure. He is convinced that everything will be well. So, John's questions about souls and the nature of their existence are answered dependent on personal feeling about the nature of humanity.
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In retrospect John seemed to feel confidently resolved about Edward’s atheism. He seems to be free of any conflict, certainly free of any animosity, about Edward's embrace of atheism. Two of the things that point to this are the fact that John keeps Edward's old baseball mitt on his desk and that he writes that he feels he has "been talking to him" his whole life.

[T]hat old glove of Edward's that I keep on my desk. No webbing at all, no pocket to speak of...

The clearest demonstration we have in the text that John seems to feel confidently resolved about Edward's spiritual condition (his atheism) is the happy time they shared playing a heated game of catch.

Edward has returned to Gilead, now the learned "Herr Doktor" and sporting an impressive mustache, having gotten his advanced degrees in ancient languages in Göttingen, Germany, a university town in Saxony. Rejected by his father's wrath over his refusal to participate in the family custom of asking a blessing before dinning, Edward and John eat a quiet meal, then walk together to Edward's hotel.

On one other day, John sought Edward out at the hotel. On a "dusty little street and a hot day" they got into vigorously throwing grounders and flies to each other. People stopped to watch the sight. Edward, with his coat off, "his collar open and his suspenders hanging down at his sides," had poured a glass of water over his head, the water running off and dripping down his mustache.

In this aspect, with water dripping, he quoted to John a portion of Psalm 133, which references brethren together in unity and precious [anointing] oil running down their beards. John lit up with recognition. He understood that Edward "knew everything [he himself] knew, every single word."

John saw Edward's knowledge two ways. As a Calvinist, he felt that since Edward knew everything, his soul was secure. He also felt that although he knew everything, his mind was not persuaded by it (the mind may not be logically persuaded but his soul may be secure through predestination). John's feelings in retrospect are the same as they were on that day: all was and would be good. 

   Behold, how good and how pleasant it is,
   For brethren to dwell together in unity!
   It is like the precious oil upon the head,
   That ran down upon the beard; ...
   Like the dew of Hermon,...
I have often thought what a splendid thing that was for him to do. I wished my father had been there, because I knew it would have made him laugh.

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