In the Task tray tool, you can set a Default Server; this default server is a server registration that points to a specific Process Manager. This defaults to the "local" Process Manager, but it can be a remote one as well.
With a Default Server set, you can set the Process Manager component's Service URL Source to Use Default. This means "use the default server specified in my task tray tool"
Another useful "trick" to use for multiple Process Manager instances is to take advantage of the Project properties EnsembleURL, EnsemblePASSWORD, EnsembleUSERID, and ServerIPAddress. By default, these are all pointing to the Default Server in the Task Tray tool.