The apache virtual host configuration has to be updated. Open up the configuration file of your virtual host, usually located in /etc/apache2/sites-available/domain-name. It should look something like this:
#NameVirtualHost *
<VirtualHost *:80>
	ServerName www.domain.org
	ServerAlias domain.org www.domain.org
	ServerAdmin name@domain.org
	DocumentRoot /var/www/path/to/site
	<Directory /var/www/path/to/site >
	Options FollowSymlinks MultiViews
	AllowOverride All
	Order deny,allow
	Allow from all
	</Directory>
</VirtualHost>
Add the following between </Directory> and </VirtualHost> (if "/conftool" is the URL and "/home/conftool/" is the directory, where ConfTool should be located).
Alias /conftool "/home/conftool/htdocs/"
	<Directory "/home/conftool/htdocs">
	Require all granted	#Note: This allows access the /home/conftool directory on Ubuntu
	Allow from all
	Options Includes FollowSymLinks
	DirectoryIndex index.php
	php_value include_path ".:/home/conftool/etc"
	AllowOverride All
	</Directory>
PHP cURL is usually not installed with default PHP installations. Install it with:
sudo apt-get install php5-curl
Adapt the following settings in /etc/php5/apache2/php.ini
upload_max_filesize 11M
post_max_size 12M
memory_limit 32M
max_execution_time 900
session.gc_maxlifetime 18000
If you have problems downloading files with IE and SSL, please try the following settings:
php_value session.cache_limiter public
php_value session.cache_expire 5
Restart your webserver
/etc/init.d/apache2 restart
and continue to testing the setup.
There is more detailed information about the 
installation of ConfTool on a server without virtual hosts available. 
This documentation was provided by Nikolaus Arnold. Thank you!