It is assumed at this point that you have properly imported the source code for your project, Configured your target platforms in eclipse, and have a workspace free of errors.
To launch a runtime workbench, you can right-click on your project and select Debug → Debug As… This dialog will show you all the different kinds of ways you can launch a program. Choose Eclipse Application, click New and accept all of the default settings. This will cause another instance of the Eclipse workbench, the runtime workbench, to start.
The launch configuration will automatically connect to the runtime workbench for the purposes of debugging. You can now go ahead and set breakpoints in your source code, just as you would for any normal Java project you launch from Eclipse.
See Java Debugging with Eclipse, by Lars Vogel - a tutorial outlining most of the functions of Eclipse JDT debugging.
See also: Plug-in Development Environment (PDE) FAQ.