To start off, below is a diagram of incoming mail flow and how all the components of our complete virtual mail system fit together. Outgoing is pretty much the same thing.
As you can see from the above diagram, all components of our email system plug into MySQL and read all our user account and domain information from a database (s). This makes administration very easy as all info is stored centrally in the database. The only thing this setup potentially lacks is a front end to make user management easier. I'm no web developer but it shouldn't be too difficult to build into a freely available CMS.
