I had to make 2 multilingual websites, so I decided to go with the developer tool and created different site.region files one for FR and one for EN. Those files connect to 2 navigation files which hold the different navigation.block structure for FR and EN. And I defined these files in the template.conf file.
The system in not entirely optimal but it works, especially if you are using a home splash screen directing to the language. (this site is still being developed http://caperia.sqsp.com)