It really just depends on your workflow. If you are working with the After Effects Plug-in, you would do your rendering within After Effects. With the Standalone Application, you would render the animation out with an alpha channel and you can import the animation into your editor program. The advantage of having one or the other is really just how you prefer to work and where you prefer to render your animation. With that said, the After Effects Plug-in does have a benefit in the sense that you are able to work with the After Effects Camera or Lights and also track your objects to After Effects layers. With the Standalone Application, you can create your animations quickly without having to run After Effects at all.
If you have both, the advantage is that you can work with the Standalone without After Effects. Then, if you need to bring the animation into After Effects, you can always apply ProAnimator in After Effects and load the ProAnimator scene that you created using the Standalone. It gives you a little more flexibility in the way you work.
Hope this helps. If you have any questions, just let me know.