If you visit your-domain.com/wp-admin/admin.php?page=w3tc_install W3 Total Cache will show you all the additional configuration information that you need. Included in that information will be some additional Nginx configurations which I've also listed below. Copy and paste it into each of your WordPress installations Nginx server blocks (a.k.a VirtualHosts).

# BEGIN W3TC Minify cache
location ~ /wp-content/cache/minify.*\.js$ {
    types {}
    default_type application/x-javascript;
    add_header Vary "Accept-Encoding";
}
location ~ /wp-content/cache/minify.*\.css$ {
    types {}
    default_type text/css;
    add_header Vary "Accept-Encoding";
}
location ~ /wp-content/cache/minify.*js\.gzip$ {
    gzip off;
    types {}
    default_type application/x-javascript;
    add_header Vary "Accept-Encoding";
    add_header Content-Encoding gzip;
}
location ~ /wp-content/cache/minify.*css\.gzip$ {
    gzip off;
    types {}
    default_type text/css;
    add_header Vary "Accept-Encoding";
    add_header Content-Encoding gzip;
}
# END W3TC Minify cache
# BEGIN W3TC Browser Cache
gzip on;
gzip_types text/css text/x-component application/x-javascript application/javascript text/javascript text/x-js text/richtext image/svg+xml text/plain text/xsd text/xsl text/xml image/x-icon;
# END W3TC Browser Cache
# BEGIN W3TC CDN
location ~ \.(ttf|ttc|otf|eot|woff|font.css)$ {
   add_header Access-Control-Allow-Origin "*";
}
# END W3TC CDN
# BEGIN W3TC Minify core
rewrite ^/wp-content/cache/minify.*/w3tc_rewrite_test$ /wp-content/plugins/w3-total-cache/pub/minify.php?w3tc_rewrite_test=1 last;
set $w3tc_enc "";
if ($http_accept_encoding ~ gzip) {
    set $w3tc_enc .gzip;
}
if (-f $request_filename$w3tc_enc) {
    rewrite (.*) $1$w3tc_enc break;
}
rewrite ^/wp-content/cache/minify/(.+/[X]+\.css)$ /wp-content/plugins/w3-total-cache/pub/minify.php?test_file=$1 last;
rewrite ^/wp-content/cache/minify/(.+\.(css|js))$ /wp-content/plugins/w3-total-cache/pub/minify.php?file=$1 last;
# END W3TC Minify core

i have both wordpress sites under the same domain in different folders.
For example Folder1 and Folder2 but this settings are like this inside my /etc/nginx/sites-available/wordpress file:

# You may add here your
# server {
#   ...
# }
# statements for each of your virtual hosts to this file

##
# You should look at the following URL's in order to grasp a solid understanding
# of Nginx configuration files in order to fully unleash the power of Nginx.
# http://wiki.nginx.org/Pitfalls
# http://wiki.nginx.org/QuickStart
# http://wiki.nginx.org/Configuration
#
# Generally, you will want to move this file somewhere, and start with a clean
# file but keep this around for reference. Or just disable in sites-enabled.
#
# Please see /usr/share/doc/nginx-doc/examples/ for more detailed examples.
##

fastcgi_cache_path /etc/nginx/cache levels=1:2 keys_zone=MYAPP:100m inactive=60m;
fastcgi_cache_key "$scheme$request_method$host$request_uri";


server {
    listen 80 default_server;
    listen [::]:80 default_server ipv6only=on;

    root /var/www/html;
    index index.php index.html index.htm;

    # Make site accessible from http://localhost/
    server_name budamail.com;

    location / {
        # First attempt to serve request as file, then
        # as directory, then fall back to displaying a 404.
        # try_files $uri $uri/ =404;
        try_files $uri $uri/ /index.php?q=$uri&$args;
        # Uncomment to enable naxsi on this location
        # include /etc/nginx/naxsi.rules
    }

    error_page 404 /404.html;
    error_page 500 502 503 504 /50x.html;
    location = /50x.html {
        root /usr/share/nginx/html;
    }

location ~* .(jpg|jpeg|png|gif|ico|css|js|woff|webm|mp4|ogv)$ {
expires 7d;
}


    location /agencia {
                try_files $uri $uri/  /agencia/index.php?q=$uri&$args;
    }

location /marketing {
                try_files $uri $uri/  /marketing/index.php?q=$uri&$args;
    }


    location ~ \.php$ {
        try_files $uri =404;
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
        fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_index index.php;
        include fastcgi_params;
        fastcgi_cache MYAPP;
        fastcgi_cache_valid 200 60m;
    }



    # Only for nginx-naxsi used with nginx-naxsi-ui : process denied requests
    #location /RequestDenied {
    #   proxy_pass http://127.0.0.1:8080;    
    #}

    #error_page 404 /404.html;

    # redirect server error pages to the static page /50x.html
    #
    #error_page 500 502 503 504 /50x.html;
    #location = /50x.html {
    #   root /usr/share/nginx/html;
    #}

    # pass the PHP scripts to FastCGI server listening on 127.0.0.1:9000
    #
    location ~ \.php$ {
        fastcgi_split_path_info ^(.+\.php)(/.+)$;
    #   # NOTE: You should have "cgi.fix_pathinfo = 0;" in php.ini
    #
    #   # With php5-cgi alone:
    #   fastcgi_pass 127.0.0.1:9000;
    #   # With php5-fpm:
        fastcgi_pass unix:/var/run/php5-fpm.sock;
        fastcgi_index index.php;
        include fastcgi_params;
    }

    # deny access to .htaccess files, if Apache's document root
    # concurs with nginx's one
    #
    #location ~ /\.ht {
    #   deny all;
    #}
}


# another virtual host using mix of IP-, name-, and port-based configuration
#
#server {
#   listen 8000;
#   listen somename:8080;
#   server_name somename alias another.alias;
#   root html;
#   index index.html index.htm;
#
#   location / {
#       try_files $uri $uri/ =404;
#   }
#}


# HTTPS server
#
#server {
#   listen 443;
#   server_name localhost;
#
#   root html;
#   index index.html index.htm;
#
#   ssl on;
#   ssl_certificate cert.pem;
#   ssl_certificate_key cert.key;
#
#   ssl_session_timeout 5m;
#
#   ssl_protocols SSLv3 TLSv1 TLSv1.1 TLSv1.2;
#   ssl_ciphers "HIGH:!aNULL:!MD5 or HIGH:!aNULL:!MD5:!3DES";
#   ssl_prefer_server_ciphers on;
#
#   location / {
#       try_files $uri $uri/ =404;
#   }
#}