ArcFM Map Server does not appear in ArcGIS Server Manager.
This is a known issue and should be fixed with ArcFM Server 9.3.1
To manually configure this, complete the following steps.
1: Open the web.config file located at C:\Inetpub\wwwroot\ArcGIS\Manager\web.config
2: Under add the following:
<extension name="ArcFMMapServer" displayname="ArcFM Map Service" capabilities=" " web="true" configuratortype="ESRI.ArcGIS.ServerManager.DefaultExtensionConfigurator" />
3: Within on the MapServer type, add ArcFMMapServer to the end of the Extensions property.