Compiling is as simple as choosing Project|Make. It's up to you if you want to compile just the selected source file or the entire project.
To run your project, choose Run|Run Project or right-click the file in the project pane you want to run and choose Run.
To set the main class and VM parameters for your project, go to the Run page of the Project Properties dialog box (Project|Project Properties).
For more information, see:
Building Applications with JBuilder: Compiling Java programs
Building Applications with JBuilder: Running Java programs