CDK supports the following views in Bioclipse: a 2D Structure Viewer, a ChemObjectTree, and a BioPolymer Tree, of which the former two are shown in this screenshot:
This shows a chemical structure with two-dimensinal coordinates. It does not allow editing, for this JChemPaint is intended.
This shows elements of a chemical object, typically a structure. Elements are then mainly bonds and atoms. When choosing an element it is highlighted in 2D Structure Viewer and JChemPaint (if open).
If you open a PDB file, you can see the hieracy of secondary structures in here.