John,
To change the servers, simply go to Settings/Monitored Nodes and "edit" the device. You have the option of setting servers to Server OR Storage. When you do this, it will move the servers in to the Storage column. The problem with doing this, though, is that you will lose visibility of SANsymphony to "its" storage as you can't show connectivity within the same columns in Analyzer. Just something to think about.
As for the direct attached FC hosts, I think the behavior you're seeing is normal. Because you have it directly attached, there is no "network" and is simply the same as local DASD from a monitoring perspective. To show "link" lines, you would need to connect both devices to a fabric.
