So you want to have different designs for the eng and ger siteaccesses, but in their siteaccess/ger (and eng)/site.ini.append.php the design is listed as site 1? Why not just change that in the siteaccess/eng (and ger)/site.ini.append.php?
As for folders, you have flexibility. Do you want all siteaccesses to start on the same top level object and have the same content, just translated? Or do you want some of all of the sites to start with different folders?
