Further question on Word order.

Thanks for answers that I recieved, I just need to clarify some
of what I was taught in Greek.

I understand fully that the word order in the Greek does not
necessarily follow our understanding.  The author could place
the subject any where in the sentence to add emphasis to it.

In an EIMI structured sentence both sides of the verb could be the subject.  
So we could write "In the beginning" or "The Word".  I understand what has 
been said about this subject so far.  The thing that I do not understand is
if one of the nouns (for lack of a better word) has an article in front of
it, I was taught that it goes to the front of the sentence.
Was I taught wrong, or as was already stated, does the prepositional phrase
cause me to modify this?

This may not have made much sense. I know what I want to say, but I am having
a hard time writing it down.  Try this and if need be I will try and 
make the muddy waters clearer.