I agree with you guys that the instructions often don't make sense when you're just getting started. Once you get the hang of it, all the mods pretty much follow the same system.
Your root folder in a fresh install is usually public_html/
Be sure to read about the template override system as well. It helps maintain the original zen stock versions of files that are edited by mods. This is good if you make a mistake, want to remove it, or want to upgrade to a new zencart version. If the files in the mod are just additions to the zen files and don't rewrite any of them, you can just upload them directly. If a file with the same name (and filepath) already exists in zen, you should create sub-directory with your template name in the location the file belongs and put the edited file there.
Here's an example from SEO urls:
Two of the files provided in the mod are:
admin/categories.php
admin/product.php
Since these two files exist in zencart, you don't want to completely lose your originals. Instead, you create a directory using your own template name like this:
admin/YOURTEMPLATE/categories.php
admin/YOURTEMPLATE/product.php
As long as YOURTEMPLATE is consistent, and you've designated it under Admin->Tools->Template Section, the files in YOURTEMPLATE will override the originals without erasing them.
This doesn't alway work with functions files, such as the file: includes/functions/html_output.php
For this one, you can first rename your zencart file as html_output.bak, then upload the new one from the mod.
Hope this helps! I had a hard time getting anybody to give me the basics when I started with zen...