This is rather a weakness on the Wordpress side I'm afraid, but there are plugins for reordering your categories. The nicest (and IMHO best-developed) one might be this one:
http://wordpress.org/extend/plugins/my-category-order/
Unfortunately, however, the changes it makes are not reflected in Atahualpa's category bar.
Flynn, I guess looking into this will take a considerable amount of coding time,
so what do you think - is there any chance of this happening?-)