Probably you want to have molecule editor functionality in your website right?
For a web application you will have to use molecule applet based editor. You will find out on our website how to include it in your page.
I assume you want to use it in a ASP.NET website. In this situation you will have to do something like this:
1. Put the marvin applet editor (MSketch) in your aspx page.
document.getElementById("some_input_type_hidden_element").value = escape(MSketch.getMol("mrv"));
MSketch is the name of the marvin applet object.
If you create an ASP.NET hidden field you might want to use instead of "some_input_type_hidden_element" something like "<%=yourHiddenField.ClientID%>" - this is because normally the generated client id for a ASP.NET control is not the same with server side id.
5. Now you should have the molecule string on server side in mrv format. So if you want to generate the molecule image you just have to follow the examples provided with JChem .NET API.
Hope this will help you...