It sounds like by enabling that other site it's changed the DocumentRoot that apache uses, from /var/www to /var/www/example/www.
You could go down the route of having multiple Virtual Servers. At it's most basic form you just need to add an entry to your /etc/hosts file mapping the hostname to your IP address then configure another site specifying the ServerName.
For a quick fix I think it would be sufficient to add the following to a new file /etc/apache2/conf.d/phpvirtualbox
Reload Apache to make the config active
Alias /phpvirtualbox/ "/var/www/phpvirtualbox/"
Options Indexes FollowSymLinks MultiViews
Allow From All
Then access it as http://server/phpvirtualbox/
sudo service apache2 reload
If you want to change the port phpvirtualbox responds on then you'll also need to modify /etc/apache2/ports.conf as you need to tell Apache to listen on port 81. Add the following to that file
and then restart Apache
sudo service apache2 restart