When is it best to render OR media encode

Adobe CS5  has the ability to encode AE comps and add to the queue without even having AE open. But i wonder what situations are better to render AE comps from the AE render queue or the standalone Media Encoder. Should a user expect better 64 bit performance from one? i know that codecs can limit that from happening, but i find that Media Encoder works all my processors into a frenzy when i render a comp from either AE or Premiere.
Would love to know whats going on under the hood so i can streamline my workflow. I have been buoyed by my recent attempts to collapse transformations and pre-render, and i want to improve my efficiency even more.

There are pros and cons to using the standalone Adobe Media Encoder. See this page for an overview of the ways of rendering and exporting from After Effects, including using AME.
One pro to using the standalone Adobe Media Encoder is that it can do two-pass encoding. So, if you're creating movies for final distribution and want to make them especially small, then you can use the standalone Adobe Media Encoder.
One con to using the standalone Adobe Media Encoder is that it doesn't have the ability to set multiple output modules for one render item. Within After Effects, you can set multiple outputs for each render item, which means that the actual rendering operation only happens once, but the encoding/compression/writing output files can happen for multiple output types from one internally held set of rendered frames. Adobe Media Encoder can't do that; if you have five output types, then the compsotion will get rendered again for each.
My workflow for creating F4V and FLV files is to render and export a losslessly encoded movie from After Effects, and have the destination for that output file be a watch folder. AME picks the item out of that watch folder and then compresses and encodes the FLV and F4V files according to the presets that I've set.

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    eg. ...."Doctor it hurts...anyone else got something that hurts?" 

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