Moon Over Manifest seems like kind of a weird title for this book—until you get to Abilene's first night at Shady's place. Her dad is in Des Moines, and she asks Shady how far away that is from Manifest. Here's his answer:
"Well, Des Moines is a lot closer than that moon. Fact is, I bet a fella in Des Moines can see the same moon you're looking at right now. Doesn't that just beat all?" (3.83)
So the moon is a link between Abilene and her dad, but it's also a link between her dad and Manifest. And for that matter, it's actually a link between everyone in Manifest, no matter the time period. In one of his letters from the front, Ned asks Jinx, "Big orange harvest moon in your piece of the sky yet?" (32.152). Everyone can see the same moon that their family and friends can see—and the same moon that everyone in the past saw, too.
In a book that's all about connections, we'd say it's an appropriate title.