Jasclipse plugin was designed to intergate *.j and *.java files in one project. Therefore you should wirte your Jasmin application inside standard Java Project. *.j files should be placed in source foulders, just as *.java files.
Before building your *.j files you must set Jasmin Nature in your project. Only Java Projects with Jasmin Nature can be build using Jasmin compiler.
To set Jasmin Nature to your Java Project, right click on its icon in Package Explorer.
Then select Set Jasmin Nature from the popup menu.
You can see that .project file has changed. A new builder and new nature have been added
Analogically, you can remove Jasmin Nature from project. The project will then no longer be build by Jasmin compiler.
After you've set Jasmin Nature to project, you can build it using standard Eclipse build commands.
Compiled classes are set in jasmin_files.jar archive, which is put in root forder of the project. The archive is also added to project classpath, so you could use its classes in *.java code.