If you want to put the pages of the site in a subdirectory you will need to update any references to the templates, css and any other linked in resources. If you want to have the same styles perform differently from the home page and the content pages you will need to manually maintain the different css files for these pages.
Will you address these issues in future releases? Considering that almost any commercial site nowadays uses at least 2 languages (local and english) this would seem like a very basic feature for a program that is called siteassist. It cannot be too complicated to hardcode a directory based layout system that allows different content versions for the same site layout? I cannot believe that I am the only customer who requests such functionality?