Sure you can. I think dragging and dropping to re-order is specifically disabled in the root playlist, but you can use the little buttons to move items up and down in the root playlist.

There was some kind of bug with re-ordering in the root playlist, something that would cause emplode to crash, I don't remember what it was exactly, and so one of the ordering methods got disabled in the root playlist.

Did I make a FAQ on that? (goes to look...)