Currently in the Apache module, there is no way to add or edit the SSLCertificateChainFile property for SSL sites. The available options are there for SSLCertificateFile and SSLCertificateKeyFile. Some operating systems will allow the SSL communication to pass without error (i.e., Windows XP) if the chain is there for particular certificate in the operating system. For other operating systems (i.e., Mac OS X and probably Linux), it would fail if the OS does not receive the entire Certificate chain.
Long story short, it would be nice to be able to specify the SSLCertificateChainFile, especially since I am using the Virtualmin and my users have access to their domains.