This is not difficult to do in eclipse. The way I did it was as follows:
1) Create the java project/structure first using a maven archetype (I can not remember the specific one, but a generic java one would do).
2) To use the JavaFX functionality of e(fx)clipse, just make sure the JavaFX libraries are included in the Libraries of you Build Path.
3) To use SceneBuilder, make sure that the executable is configured in Window|Preferences|JavaFX screen.
NB: if you are using a java version that has javaFX already in it (e.g. java 8 or a recent java 7 releaase) then you don't need to add a separate JavaFX library in the build path. This was only necessary when JavaFX was not bundled with the rest of the JDK, which is no longer the case.
Good luck.
- chooks