Thats what the minor is for. If you have a look at the source:
Lua Code:
local oldminor = self.minors[major]
if oldminor and oldminor >= minor then return nil end
So the one with the highest minor gets loaded in the end and all other instances are deleted/overwritten.
Also see here:
http://www.wowace.com/addons/libstub/
Cheers