I've never used Apache on Windows, but I assume that it is structured the way that Apache themselves suggest/provide. RedHat (and derivatives e.g. CentOS) also use the configuration that I imagine you are familiar with.

However Debian (and it's derivatives such as TurnKey and Ubuntu) does stuff differently (and IMO better). Instead of having a monolithic httpd.conf; the conf file is broken up into multiple purpose specific files.

So if you want to add a new port, you add it to /etc/apache2/ports.conf if you want to edit a module config; you edit /etc/apache2/mods-available/module-name.conf. If you want to enable/disable a specific module the you use the a2enmod/a2dismod module-name commands. They just create/delete symlinks between /etc/apache2/mods-enabled/module-name.conf and /etc/apache2/mods-available/module-name.conf. Same for virtualhosts or site config (what you are after). They all reside in /etc/apache2/sites-available/site-name.conf and are enabled/disabled with a2ensite/a2dissite site-name.

So if you want to adjust the Apache config for ownCloud; you'll want to edit /etc/apache2/sites-available/owncloud.conf

To test what you've done, reload Apache:

service apache2 reload

Another word of warning (for Windows users). Whatever you do DO NOT edit a Linux configuration file in Windows Notepad. It mangles the files and makes them essentially unusable (even though they'll look fine in Windows). Nano is pre-installed in TurnKey and is as easy to use (IMO) as Notepad. Or if you want to edit files in Windows, get yourself a copy of Notepad++.