I basically move books over a few at a time, then when I finish reading them, I put them into collections (if I think I might read them again someday) or delete them.
At first that worked pretty well, but I haven't been reading all the ones that I put on it, probably only half. That's starting to leave a lot of clutter. And I only have 250 books on it.
Anyway, the order isn't random, it's basically based on the last time you read it. So if you read a series in order (like I have), then it's the first one down at the bottom and the last one at the top.