Try changing the name of one node, and the other will update itself. The bytecode branch of the containment tree is not supposed to show every class available according to the classpath. Instead, only the bytecode classes which are 'one step away' from classes in the source code are included in the bytecode branch. This means that there is a pretty good chance that you can quickly locate the class you are looking for, assuming you have already used it elsewhere. On the odd occasion when you need to derive from a bytecode class which has not yet been loaded, use the 'Load VM Class' option on the file menu to bring it into play.
New classes have to be made in the containment tree, and then dragged to the diagram.
You can always drag a class to another package after you have created it. The reason is that simply making classes into tables and non-transient fields into columns does not achieve much. Each time the model changes the SQL breaks. It would be possible to generate all of the SQL, including DDL, resulting in an object-relational mapper, but this way of working has largely been superceeded by letting J2EE handle persistence. In other words, you can load as many classes as you like, but you can only edit the first 10.