Hi!
You use JUnit together with TestFX to test your JavaFX applications. You can use a separate project for your test source code, but it is very common to put the test source code in the same project as the main source code resides. Another common pattern is to split your source directories into a main directory (for the actual application code) and a test directory (for the test code).
You actually run the tests with a run target (right click on source editor, run as -> junit test).
Regards
Benjamin