EasyEngine is using Nginx as webserver it doesn't use/support mod_rewrite module. Nginx has it's own rewrite set of rules.
What are you trying to do? If you create a new website with EE commands, like
ee site create mydomain.com --wp
It will create a Wordpress based website including database and it will have proper permalinks setup for you, no need to use any extra modules.
So please let us know what is it you're trying to do? Perhaps then we can help you more.