I did install squirelmail in the directory specified by the perfect server guide for Ubuntu 9.04. I do not know what FTP method I am using. I think the problem is in Apache somewhere. It is not allowing me to cross over directories. The site with the symlink is in /var/www/clients/client1/web5/web and webmail has a symlink in /var/www/webmail to /usr/share/squirrelmail/ I think maybe this is where the problem is...I used the Ubuntu 9.04 perfect server guide, if that helps.
Sorry I am such a n00b at this, but I am learning a ton thanks to everyone here at howtoforge!