I found that I can sort on the Reader when it is plugged in without using sync.
I view the collection in the Reader and drag and drop into the place i would like it. This works well for when I am just adding a book or two and want to be quick. Or when I want to change the order of what i want on the first page of a collection. (hopefully, this isn't what you have been talking about and I just misunderstood.)
