Oh my goodness. Well here is why there was such a confusion. The lady that instructed me on how to create a website has me generating my templates like this.
{{ag_header}}
{{ag_headerlinks}}
{{ag_topmenu}}
{{ag_leftcolumn}}
{{ag_rightcolumn}}
{{ag_infosli}}
{{ag_quicklinks}}
{{ag_newsheader}}
<autolink>[*content*]</autolink>
[!bannerrotator? &position=`1`!]
{{ag_footer}}
She would have me take the web page cut it up into sections and create chunks that would create the whole website.
It would kind of stink to have to completely redo all that plus a quick test i am already noticing more things breaking than working.
(for instance now Latest News background image no longer shows now for some reason and its like that for the headers on all the pages now)

is the one referring to. Which is just making me pace in circles pull my hair out and chain smoke my cigarettes.
However if that is the proper way and the right way than I guess I will have to just suck it up.
I do apologize for the inconveniences, the lady that had taught me the basics of MoDx was a friend of mine from his church, and it would appear I was instructed wrong. However that does stink because I really liked how clean that all looked to be honest that was one of the first things that I liked about it.