Multi Site and Clean URLs

I know this has been asked before but I can't find something like my configuration and it seems that I need this to enable "teaser thumbnail".

I run an apache web server, I have full access to it.

One of my clients has two drupal sites configured as multisite. None of them is in the root of the drupal instalation.

So I have

/var/www/html/client (drupal root)
-----> /sites/www.site1.com
-----> /sites/www.site2.com

and in apache:

<Virtual Host *>
DocumentRoot /var/www/html/client
ServerName www.site1.com
</VirtualHost>

<Virtual Host *>
DocumentRoot /var/www/html/client
ServerName www.site2.com
</VirtualHost>

serves the right site.

But I don't understand how to configure the rules for clean urls to work.

Adding

<Directory /var/www/html/client>
  RewriteEngine on
  RewriteBase /
  RewriteCond %{REQUEST_FILENAME} !-f
  RewriteCond %{REQUEST_FILENAME} !-d
  RewriteRule ^(.*)$ index.php?q=$1 [L,QSA]
</Directory>

shows me apache default page for the main page and a 404 error for anything else. I've tried several combinations of RewriteBase and RewriteRule with no luck.

Before you ask: mod_rewrite is enabled, AllowOverride is currently set to none but I can change it.

Thanks!