There is no right or wrong. Apache has one global config file, which
typically is the default or specified in the startup script.
This file then uses one or more secondary config files and directories.
Different Linux distributions use different default include
On CentOS I think for example you would put a file (named like your
domain but can be anything) in /etc/httpd/conf.d/example-com.conf: http://wiki.centos.org/TipsAndTricks/ApacheVhostDir