Currently Being ModeratedNov 27, 2012 4:34 AM (in response to BioRich)
Careful when manually editing configuration files in /Library/Server/Web/Config/apache2/sites. There are a variety of parameters that will be overwritten by Server.app. Among them ServerName, Port, AuthName, AuthType, Limit, Require, Options, AllowOverride and some more.
Your safest bet is to add an include statement to the end of the configuration file in /Library/Server/Web/Config/apache2/sites. Something like:
Next include all personalised parameters in the included file. This will make sure your changes are read by Apache and not overwritten by Server.app
If you need to cater to more advanced configurations, you should have a look at webapps (see man webapp.plist).