I recommend to take a look at JChem Base examples.
It demonstrates how you can integrate MarvinSketch and MarvinView into substructure search.
Actually, there are two ways:
1. Generate image for each structure and insert it into the proper cell on the generated html. By clicking on the image, it is replaced to a MarvinView applet instance. The Ajax example follows this way.
2. Insert a multicell MarvinView applet. The table is rendered by the MarvinView. It display either the structure, IUPAC name, SMILES string and chemical structures. JSP based examples (like simple example) follows this way.
The source of examples you can find in the JChem package.
To be more familiar with MarvinView customization, I recommend to check also MarvinView applet examples on Marvin site: