Здравствуйте, у меня на проекте следующая структура папок:

engine/
__index.php
webroot/
__images/
__css/
__cms/
______engine/
_________index.php
______webroot/
_________images/
_________css/
_________js/
___________uploader/
_____________upload.php
___________jquery/
others/

И такой конфиг:
server {
listen 8080;
server_name glinka.fm;
root /home/renat/www/glinka;
index index.php index.html;

location / {
try_files /webroot/$uri /engine/index.php?$args;
}

location ~ ^/cms/?(.*)$ {
try_files /webroot/cms/webroot/$1 /webroot/cms/engine/index.php?$args;
}

location ~ \.php$ {
try_files $uri /webroot/$uri =404;
include fastcgi.conf;
}
}