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I have already gone through 4 tutorials here and the internet and I am obviously not getting it as all say the same thing. Just talked to 4 other new zen cart people and they aren't either.
I had no includes/languages/ENGLISH/CUSTOM directory I take it I create one?
I take it we can't just replace the header.php as we would if were changing an html file.
I have replaced the script, ensuring the quotes were in tact. Nothing changed at all. I edited in notepad+++, saved, then uploaded it to the custom folder I created.

The "CUSTOM" directory mentioned in the various tutorials is the name you select when you create your own custom template. It's the foldername into which you create your own custom template. Then you use that same foldername in the appropriate override locations (such as the one you quoted) to save your edits to the files you customize. This makes your future upgrades much easier than if you were to directly edit core files, since all your custom changes are easily identified.

To create your own template, you need to create the folder, and then create a template_info.php file which contains some primary information about the template. Then you log into your Admin area and select that template from the Tools->Template Select menu. At that point all your "CUSTOM" folders (again, that's the folders matching the name of your template's folder) will be able to take over as overrides to take precedence ahead of the normal system defaults contained in the original code.

The concepts of creating your own custom template and of using overrides are all discussed at length in several Tutorial/FAQ articles.