When you think of CVS commands within jCVS, you should think in terms of two categories: those that operate on a checked out working directory, and those that don't. For instance, commands that operate on a checked out working directory include status, tag, diff, and update. Checkout, export, and import are commands that do not operate on working directories.
Commands that operate on working directories are run via the project Window. Commands that do not, are all run via the main window, since there is not working directory to be displayed in a project window.