Um, you don't have to change the shape, just change the center point. The center point can be anywhere in the shape. Click on the "set center point tool", then where you want that point to be (for example bottom left looks like it has the most room).
Look at my map, I have lots of points that are moved:http://warlight.net/SinglePlayer?PreviewMap=17952
I guess you cannot see center point on that link, but if you notice many factories would overlap if the army number was simply centered.
EDIT - I realize you may be referring to the Bonus number, not territory army number. If so, just move your Bonus Link shape somewhere else.
Edited 12/23/2013 19:09:39