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

i'm using cs6.  i've noticed can import ae files prpro , vice versa , can render media encoder.  1 of these better render out of other?  example, if you're using animation ae in prpro better render animation , import video file prpro or import ae project file prpro , render @ once?  or better render media encoder?  or application based? 

this more of question of workflow.  different workflows require different ways of working in ae.  what's typical workflow you?

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