I am using CentOS 7 for my installs, i don’t use Ubuntu so i can’t speak for its configuration. I use a script that i have written to automate the setup of WordPress and deploy Nginx confs as well as setup mysql db. My script is on github for CentOS 6 and it is beta for CentOS 7, if you are running those it will help you out but if you are running Ubuntu i would suggest looking at rtCamp scripts for WordPress.

My directory structure always looks like this /var/www/$DOMAIN/htdocs with WordPress install inside of htdocs and wp-config.php moved to /var/www/$DOMAIN/.

domain 1 WordPress - copied and pasted from working server

server {

        server_name domain1.com www.domain1.com;

        access_log   /var/log/nginx/domain1.com.access.log;
        error_log    /var/log/nginx/domain1.com.error.log;

        root /var/www/domain1.com/htdocs;
        index index.php index.htm index.html;

        location / {
                try_files $uri $uri/ /index.php?$args;
        }
        location ~ /fpm/status/(.*) {
        include fastcgi_params;
        fastcgi_param  SCRIPT_NAME  /status;
        fastcgi_pass $1;
        }

        location ~ \.php$ {
                root /var/www/domain1.com/htdocs;
        fastcgi_pass   127.0.0.1:9000;
        fastcgi_index  index.php;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        include        fastcgi_params;
        }


}

domain 2 WordPress - copied and pasted from working server

server {

        server_name domain2.com www.domain2.com;

        access_log   /var/log/nginx/domain2.com.access.log;
        error_log    /var/log/nginx/domain2.com.error.log;

        root /var/www/domain2.com/htdocs;
        index index.php index.htm index.html;

        location / {
                try_files $uri $uri/ /index.php?$args;
        }
        location ~ /fpm/status/(.*) {
        include fastcgi_params;
        fastcgi_param  SCRIPT_NAME  /status;
        fastcgi_pass $1;
        }

        location ~ \.php$ {
                root /var/www/domain2.com/htdocs;
        fastcgi_pass   127.0.0.1:9000;
        fastcgi_index  index.php;
        fastcgi_param  SCRIPT_FILENAME  $document_root$fastcgi_script_name;
        include        fastcgi_params;
        }


}