There seems to be many different ways to get a result. Here is one that works for me (I have three sites off one root and furls working for all of them).
1. Install modx into a subdirectory of the root (eg /var/www/mysite) using the standard install (lankford, I don't believe advanced install is needed).
2. Put .htaccess in that subdirectory but with a RewriteBase of / (yes, this is not what the doco says but it works). This is what my .htaccess looks like:
RewriteBase /
# Rewrite www.domain.com -> domain.com -- used with SEO Strict URLs plugin
RewriteCond %{HTTP_HOST} .
RewriteCond %{HTTP_HOST} !^mysite\.com [NC]
RewriteRule (.*) http://mysite.com/$1 [R=301,L]
3. Set up furls as per the rtfm (or this is how I did it for Articles, but it is the same process - just clarified for my benefit:
http://rgissing.com/blog/modx-revo-friendly-urls/)
4. Add an entry for mysite.com in /etc/apache2/sites-available. I covered this earlier in this thread for those who, like me, have access to the filesystem. For others, provided you have access to cpanel, I
believe the same thing can be done using that tool (see this thread:
http://forums.cpanel.net/showthread.php?p=1450471). But I have not tested this.
5. Restart Apache.