The main theme of A Prayer for Owen Meany is religious faith--specifically, the relationship between faith and doubt in a world in which there is no obvious evidence for the existence of God. John writes on the first page of the book that Owen Meany is the reason that he is a Christian, and ensuing story is presented as an explanation of the reason why. Though the plot of the novel is quite complicated, the explanation for Owen's effect on John's faith is extremely simple: Owen's life is a miracle--he has supernatural visions and dreams, he believes that he acts as God's instrument, and he has divine foreknowledge of his own death--and offers miraculous and almost undeniable evidence of God's existence. The basic thematic shape of the novel is that of a tension being lifted, rather than a tension being resolved: John struggles throughout the book to resolve his religious faith with his skepticism and doubt, but at the novel's end he is not required to make a choice between the two extremes: Owen's miraculous death obviates the need to make a choice, because it offers evidence that banishes doubt. Yet John remains troubled, because Owen's sacrificial death (he dies to save the lives of a group of Vietnamese children) seems painfully unjust. John is left with the problem of accepting God's will. In the end, he invests more faith in Owen himself than he invests in God--he receives two visitations from Owen beyond the grave--and he concludes the novel by making Owen something of a messiah, asking God to allow Owen's resurrection and return to Earth.
Of course, the thematic development of the novel is somewhat more complicated and less neat than that, and the presentation of religion in the book is continually undercut with irony and the constant presence of sex. Further the thematic development of the book is also inconsistent and indirect, in part because we are never able to gain a secure purchase in John's mind: he is such a reticent narrator that it is difficult to tell exactly where he stands during much of the novel, which often blurs our sense of his struggle with faith and doubt. This ambiguity underscores the important point that Irving's basic intention for his novel is not to present a philosophical meditation on the nature of God, but rather to tell a gripping story. Beyond a certain point, it is simply not rewarding to analyze the book's explicit philosophical content as it is embodied in the book's plot. Far richer and more nuanced is the book's roster of symbols and motifs, many of which are explicitly discussed by John in key passages of the novel.
The most important symbol in A Prayer for Owen Meany is Owen himself; Owen embodies the relationship between the natural and the supernatural that is at the heart of the novel's main theme. With his tiny, dwarfed body, his weirdly glowing skin, and his ethereally nasal voice (always represented in the book by capital letters), Owen is not entirely of this world--his appearance validates his bizarre spiritual life, in which he seems to be in direct communication with God. On the other hand, Owen is very much of this world: he grows up in a granite quarry, and his name is "Meany"--a word signifying commonness and smallness. For all his eccentricity, Owen in many ways represents the spiritual condition of humankind; the difference between most people and Owen is that Owen knows he is the instrument of God. His fatalistic faith centers around his prophetic knowledge of his own heroic death, for which he prepares all his life. Owen believes that everything that happens is the will of Godhe continues to believe this even when he accidentally kills John's mother with a foul ball he hits at a Little League game.
Another key motif in the book is that of armlessness and amputation. The book abounds with images of people and objects that lack body parts, most often arms: Watahantowet's armless totem, the armless dressmaker's dummy, the declawed armadillo, Lydia's amputated leg, John's amputated finger, the armless statue of Mary Magdalene, and Owen himself, who loses his arms in the explosion that causes his death. In the book, as John often thinks to himself, armlessness represents a number of different ideas: the helplessness of people against the injustice of fate; the pain caused by that injustice; the loss of loved relations or possessions; the surrender of the individual to God (in the sense that God "takes" one's arms, using them as his instruments--as when Owen swings the fatal bat).
Structurally, the book favors a rambling, expansive narrative that skips from memory to memory and scene to scene apparently at the whim of John's first-person narration. The memoir-like form of the book means that much of John's experience plays out concurrently with important events in American history--the Kennedy assassination and the Iran-Contra scandal, to name two--and John's commentary about these events forms an important sub-theme of the book. John's obsession with America often overshadows his narrative focus on his childhood and his thematic focus on religion, and he frequently loses sight of his story in long diatribes against the Reagan administration. The book's psychological study of John is somewhat hazy, because John's nature as a narrator is to keep the focus off of himself; but it is clear that, for all his protestations of religious faith, he is a deeply damaged and bitter man as he narrates the story. Throughout much of the book, John's anger about America seems to stem from his feelings of loss and outrage about the death of Owen Meany; whatever else has happened to him, it is clear that he has been unable to move beyond the events that he narrates in the novel. He continues to live in the past.
I think that Owen's being swaddled too tightly to move his arms in "The Little Lord Jesus" is another instance of the armlessness motif, especially considering the religious setting of the pageant.