If you want jPages to use Animate.css animations you will need to add the link for the file in the head of your file, however the plugin already adds the required "animated" class to the items, so all you have to do is to choose an entrance animation class and pass it to the plugin. You can customize these animations in the style sheet or even create new ones.
Keep in mind that jPages currently only supports entrance animations!
If the browser doesn't support CSS3 Animations or if you just don't set any animation, jPages will fallback to the jQuery fadeIn effect. You can customize the speed of this effect in the parameter "fallback". See the example here.