Use drag and drop to change the order of your categories.
Click and hold your mouse on a category icon on the tree and then:
To move your category below another category in the tree, move it so you see a line below your target category.
To move your category to within an existing section in the tree, drag it on top of your target category:
Note: Currently, a category cannot contain products AND sub-categories, so be careful when moving your categories around the tree.