The eclipse plugin generates warnings on all lines where you violate the dependencies defined in /jlayercheck.xml (in the project root). You have to put the configuration file there and activate the builder by right clicking on the project in the package explorer and clicking on "Add/Remove JLayerCheck Nature". Afterwards the "JLayerCheck Builder" should occur in the builders section of your project.
The name of the eclipse update site to install the plugin is:
The warning will appear on the lines that violate the architecture:
The tooltip of the warning markers and the problems view can be used to get detailed information of the dependency violations: