Using code from this tutorial:
http://code.makery.ch/java/javafx-8-tutorial-part4/

If you have FXML file with 'stylesheets' attribute set in root pane:

    <AnchorPane prefHeight="363.0" prefWidth="693.0" stylesheets="@DarkTheme.css" ...

Then you load the FXML with this code:

    FXMLLoader loader = new FXMLLoader();
    AnchorPane personOverview = (AnchorPane)loader.load(getClass().getResource("view/PersonOverview.fxml").openStream());

    this.rootLayout.setCenter(personOverview);
    ...

You would get error message in eclipse output screen like this:

    null/DarkTheme.css
    Dec 09, 2014 1:42:54 AM com.sun.javafx.css.StyleManager loadStylesheetUnPrivileged
    WARNING: Resource "DarkTheme.css" not found.


But there will be no error if you do it like this:

    FXMLLoader loader = new FXMLLoader();
    loader.setLocation(MainApp.class.getResource("view/PersonOverview.fxml"));
    AnchorPane personOverview = (AnchorPane) loader.load();

    this.rootLayout.setCenter(personOverview);
    ...

and if you use static method FXMLLoader.load(java.net.URL location):

    AnchorPane personOverview = FXMLLoader.load(getClass().getResource("view/PersonOverview.fxml"));
    this.rootLayout.setCenter(personOverview);
    ...