Can you have two directory rewrite rules in one configuration?

In /etc/httpd/conf.d for custom conf file where you have multiple sites and databases but with different systems installed in non root folders can you declare more than one rewrite rule like below? I am getting errors with xml not being read to install extensions for joomla and not finding it in tmp folder even though permissions and ownership are correct so think it must be the conf file settings. I don't use .htaccess. Yet if I install extensions via a system install extension it works. RewriteEngine on RewriteBase / RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d #RewriteCond %{REQUEST_URI} ^/(.*)$ RewriteRule ^(.*)$ index.php?q=$1 [L,QSA] RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteCond %{REQUEST_URI} !=/favicon.ico RewriteRule ^index.php [L] RewriteEngine on RewriteBase / RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d #RewriteCond %{REQUEST_URI} ^/(.*)$ RewriteRule ^(.*)$ index.php?q=$1 [L,QSA] RewriteCond %{REQUEST_FILENAME} !-f RewriteCond %{REQUEST_FILENAME} !-d RewriteCond %{REQUEST_URI} !=/favicon.ico RewriteRule ^index.php [L]