You are looking in the right place... The files in the admin and includes folders are files that are included in the core code of Zen Cart 1.3.8a. You need to update the files in ZC with these new files (you want the files to be overwritten but not the entire directory, there are many other much needed files in these directories). If you have not installed any other modules before this one you can safely over write the files directly.
There is one folder you will need to change the name on. It is includes/templates/YOUR_TEMPlATE/ you need to change the "your_template" to the name of your template.
All this is included in the readme.txt files. I'd read those very carefully.
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