I think you mean the order of the menu items.
At the moment the menu items are sorted alphabetically.
You can change this as follows:
Open $:/plugins/tongerner/topmenu/menu-template
Change the line
<$list filter="[all[current]tagging[]]" template="$:/core/ui/ListItemTemplate"/>
to
<$list filter="[all[current]tagging[]sort[order]]" template="$:/core/ui/ListItemTemplate"/>
and add to all menu item tiddlers a field 'order' containing the item position. The the menu items are then sorted according to the number in the order field.
Hope that helps.
Cheers,
Ton