Multi site with multi language problem

I am struggling with setting up multi site with one multilingual site.
To be clear the structure should look like:

domain1.com = 1st website
domain2.com = 2nd website
domain3.com/en = 3rd website in english
domain3.com/de = 3rd website in german

for 3 domains I used gateway manager plugin and it worked pretty good. but once I installed babel to handle multilanguage everything goes messed up. Does anyone know how to set rewrite rules in .htaccess? I guess that is the only problem.