Is there a best way to render? (Not asking about codecs)

I'm using CS6.  I've noticed you can import AE files into PrPro and vice versa and you can also render with Media Encoder.  Is any one of these better to render out of than the other?  For example, if you're using an animation from AE in PrPro is it better to render the animation and then import the video file to PrPro or to just import the AE project file to PrPro and render it all at once?  Or is it better to render everything with Media Encoder?  Or is it all just application based?