As I needed it for tomorrow I started researching how to change the .htaccess, and found the answer after much wandering, we locate where the .htacess first, and as I was using BitNami, the .htacess was in a different place. But I could find!
So I had to find this:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>
And put this code before:
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_URI} ^/REPLACE WITH SUB DIRECTORY NAME/(.*)$ [OR]
RewriteCond %{REQUEST_URI} ^/REPLACE WITH SECOND SUBDIRECTORY NAME/(.*)$ [OR]
RewriteRule ^.*$ - [L]
</IfModule>
And problems solved!
Let this topic in the right place, I looked at many, many places here, but none gave me the answer I needed!
Answer found here:
https://stackoverflow.com/questions/5754548/non-wordpress-files-in-wordpress-installation-directory