The documentation is common for both JBDE1 and JBDE2, JBDE2 has a nicer interface and it has some extra features (saving the diagram as an image and printing the diagram) but otherwise they are much the same. The JBDE file format is the same for both versions (you can save a diagram in one version and then edit in the other one).
After the program is launched, a window with a block diagram will show up. You can choose start to edit a new block or bubble diagram from the File menu.
Everything (editing, adding, removing items) is done by using popup menus. Alternatively, you can edit an item by double-clicking it. Almost every item can be dragged (excepting connections, you can only redraw a connection).
A block diagram has blocks, block ports, diagram ports and connections.
A bubble diagram has states, transitions and diagram ports.