Multiple wordpress sites windows server pretty permalinks

I was asked to use pretty permalinks (as we should) on a blog located inside a /blog directory. The problem is that the server is Windows and the site at the root is also a wordpress. Currently, it is working by having a permalink on each site (one on the root and one on the sub-directory).

I barely know a thing about windows’s web.config, but I read that I should have only one of those on the root, pointing to the blog. However, when I try and remove the sub-directory one and change the permalink on WordPress, it creates its own file again, where I deleted the previous.

Have anyone gone through this problem before?

root:

<?xml version="1.0" encoding="UTF-8"?>
<configuration>
    <system.webServer>
        <rewrite>
            <rules>
                <rule name="Redirect to WWW" stopProcessing="true">
                    <match url=".*" />
                    <conditions>
                        <add input="{HTTP_HOST}" pattern="^example.com$" />
                    </conditions>
                    <action type="Redirect" url="http://www.example.com/{R:0}" redirectType="Permanent" />
                </rule>
                <rule name="Redirect to WWW Another domain" stopProcessing="true">
                    <match url=".*" />
                    <conditions>
                        <add input="{HTTP_HOST}" pattern="^anotherdomain.com$" />
                    </conditions>
                    <action type="Redirect" url="http://www.example.com/{R:0}" redirectType="Permanent" />
                </rule>
                <rule name="Redirect to Another Domain" stopProcessing="true">
                    <match url=".*" />
                    <conditions>
                        <add input="{HTTP_HOST}" pattern="^www.example.com$" />
                    </conditions>
                    <action type="Redirect" url="http://www.example.com/{R:0}" redirectType="Permanent" />
                </rule>
                <rule name="wordpress" patternSyntax="Wildcard">
                    <match url="*"/>
                    <conditions>
                        <add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true"/>
                        <add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true"/>
                    </conditions>
                    <action type="Rewrite" url="index.php"/>
                </rule>
            </rules>
        </rewrite>
    </system.webServer>
</configuration>

sub-directory:

<?xml version="1.0" encoding="UTF-8"?>
<configuration>
  <system.webServer>
    <rewrite>
      <rules>
            <rule name="wordpress2" patternSyntax="Wildcard">
                <match url="*"/>
                    <conditions>
                        <add input="{REQUEST_FILENAME}" matchType="IsFile" negate="true"/>
                        <add input="{REQUEST_FILENAME}" matchType="IsDirectory" negate="true"/>
                    </conditions>
                <action type="Rewrite" url="index.php"/>
            </rule></rules>
    </rewrite>
  </system.webServer>
</configuration>

Also, both index.php are like so:

define('WP_USE_THEMES', true);
require( dirname( __FILE__ ) . '/wp-blog-header.php' );