With the new addon, www.domain.com, as far as MODx is concerned, or anybody for that matter, your new site exists by itself and not in a sub-directory. That's a secret between you and your server, that is, where your physical files are (
www.main-mother-account.com/domain/)
So MODx should be made to treat your site as a true TLD, hence just a
slash will do. Don't include the
sub-directory
RewriteEngine On
RewriteBase /
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
If you wanted another MODx installation within your new domain, that is, www.domain.com/new-modx/ (physically located in www.main-mother-domain.com/domain/new-modx/) then you would need it in the .htaccess file. and don't forget,
two slashes
RewriteEngine On
RewriteBase /new-modx/
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]