Javascript deprecated

Thanks for the prompt reply Paul, and my apologies for not really understanding what I am doing.

From your reply, I believe what you are saying is

1) I have to "point" or "load" my jquery library
2) I would do this in a footer or header, just like I would point or load CSS or load an image.

If this is correct, then what I am asking is:

1) Why am I using a framework when I have to point and load all my CSS and variables and more for every page? Is this not what CI is for, to take out the redundancy of retyping and retyping? Or am I confusing CI for something like a page template, like the Blade templates in Laravel?
2) That said, what I am trying to do, I think, is actually point or load my Jquery, which is what I think you are also trying to tell me to do. I can load this in every view. Is there a way to pre-load in a controller or ??

My directory tree is:

application
assets
 - css
     -- nothing here (meaning there is no style.css or any other files)
 - js
     -- jquery (which I copied from the original file and renamed it)
     -- jquery-10.10.2 (the file I downloaded)  

system
  - libraries
    -- Javascript
       --- Jquery (I think this came with my original CI install)

The whole point of this exercise is I am trying to setup a form and this seems the way most of the online tutorials are doing it. Of course, as usual, code examples are buggy and I am not the brightest bulb on the Christmas tree, but I am still at it.