Well hopefully you are a LONG way from drastic action.
I think you need to understand how the override system works, and what the purpose of the custom template is.
In a fresh install of zencart, the system (certainly on the webshop side of the software) will compile the web pages using the PHP files in the TEMPLATE_DEFAULT template.
So... if you have not created your custom template, then zencart will call (FOR EXAMPLE)...
includes/templates/template_default/common/tpl_main_page.php
... when it builds up the main page.
But you then decide you want to make some customizations to the main page, and this will require making some changes to:
includes/templates/template_default/common/tpl_main_page.php
So what you do is make a COPY of tpl_main_page.php
(You would typically do this on your hard drive - because that is where you should do the editing as well)
You then EDIT the file and save it on your hard drive.
Now, that EDITED file must not overwrite the CORE (default) file.
So, you would put it into the corresponding OVER-RIDES folder in your own template.
I don't know what you have called your custom template, so I will refer to it as YOUR_TEMPLATE
The location of your newly edited file will be:
includes/templates/YOUR_TEMPLATE/common/
... but you may not yet have a folder called "common" inside YOUR_TEMPLATE...
... so you create one...
And then you ftp tpl_main_page.php to THAT folder...
includes/templates/YOUR_TEMPLATE/common/tpl_main_page.php
The ORIGINAL file (from which you made a copy) is left untouched in its original location:-
includes/templates/template_default/common/tpl_main_page.php
Now... zencart is quite clever...
It will look FIRST for your override file(s) when it starts to compose a page.
If it finds the overrride, it uses the override file...
includes/templates/YOUR_TEMPLATE/common/tpl_main_page.php
If it does NOT find an override, it uses the CORE file
includes/templates/template_default/common/tpl_main_page.php
All you need do now, is what we explain above, regarding your js files.
Finally, I hope you also realise that having the JS files is meaningless unless there is some PHP code somewhere that uses them...