RPG Next Gen allows you to modify the library list of a connection on two occasions:
Properties view
To change the user part of the library list after connection creation you need to bring up the Properties tab (a.k.a. Properties view). To bring up the Properties view select Window → Show View → Other → General → Properties. Next select the connection name in the Remote Explorer view. This will then allow the properties for that connection to be displayed. There are three sections in the Properties tab - Common, Listed Libraries, and Library List. Select the Library List tab. From here you can use the add/remove buttons to alter the list of libraries shown. The changes to the library list are immediately in effect without explicitly closing/opening the connection.