Currently having a multi lingual site like this is not supported in SiteAssist Pro. You would need to manage the sub sites yourself to achieve this result.
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.