
  How can I modify the rule so that it only affects maindomain and not subdomains?


You can add a new condition based on host name:

RewriteEngine on

RewriteCond %{HTTP_HOST} ^(?:www\.)?mainsite\.com$ [NC]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule . index.php [L]


Redirect all requests to index.php except subdomains
I hear people say "I can get this or that out of these skins" but how do you know what you can get out of a skin?
