The software is complex enough to need documentation. Currently, the majority of the pages on this site contain information specific for the VisualWorks version of JNIPort. Large parts of what you find here is copied from Chris Uppal's documentation of JNIPort for Dolphin Smalltalk, with changes where appropriate. The complete online documentation of JNIPort for Dolphin Smalltalk is currently only available at the Internet Archive: Wayback Machine, but it can also be downloaded for offline reading from the Download page.
You should start with the introduction, which also includes a very simple example, and the walkthroughs of installing and configuring JNIPort in the platform specific sections. You might also like to look at some more complete examples, and have a look at the problems and limitations of JNIPort.