The first requirement is to make sure that the files (the agent packages and any software packages) that need to be downloaded to the device can be downloaded using FQDN. To do this, NS requires the usage of a package server that has a full name set in its computer settings.
The second requirement is to change the web.config on the Mobile Management Server. The path (assuming the default location) is:
C:\Program Files\Symantec\Mobile Management\MobileManagement\web.config
Edit this file and change the DnsSuffix entry to have the domain name suffix. For example, if your FQDN is “ns-mss.symantec.com”, your DNS suffix is “symantec.com” and the entry in the web.config would be:
<add key="DnsSuffix" value="symantec.com"/>
The only aspect that doesn’t change is the Mobile Agent Download URL on the Mobile Agent Install page of the console does not reflect the FQDN, so currently the end user must know to enter the FQDN in Pocket Internet Explorer on the device.
Finally, the below URL may provide a better understanding of how the product works in a networked environment
http://www.symantec.com/docs/HOWTO38652
Thanks for your help Mark!