As you know there is a language override in Joomla that is also used for translations. What is the difference between this and the language stuff you have in EB?
I guess during an update of EB, the language stuff in EB will also stay as it is a DB-based override no?
You just need to use translation feature of EB. EB is smart enough so that when you upgrade to newever version, the modified language strings will be kept so that we don't have to re-do it every time you upgrade EB