I use cpanel and when I setup a subdomain it automatically creates a folder for it under the public/html. Every subdomain is its own folder.

Now in the video you have very long folders destinations.But doesn't that also make for very long urls for the users.

If I was to create a subdomain named test and put it in the folder of public_html/subdomains/test My url would be

test.domain.com/subdomain/test so the user would have to type in that to find the site?

I want my user to be able to type subdomain.domain.com and it go right to that slave site. I don't want to have to create redirects for everything.

I understand the point of not wanting to overwrite the master but,

public_html
-master
-subdomain1
-subdomain2

If I have this setup in cpanel I am ok right?

In our video we do NOT create the subdomains inside the /public_html
We recommand to install beside.

if you have www.domain.com that is your primary domain attached to the cPanel then you use the /public_html
For the "Addon domain" and "Sub-domain" we recommend to use the structure

www.primarydomain.com => /public_html
www.domain.com => /domains/domain.com/public_html
sub1.domain.com => /domains/domain.com/subdomains/sub1/public_html

With this structure all the domains and subdomains have their own directory and you can also have confidential directories beside.

Review the tutorial video 0.b - slide 21-24

When your cPanel allows it, never create subdirectories in your /public_html for the subdomain or domains. The Search Engine could reference those subdomains or domain like a subdirectory of your primary domain.

www.domain.com => /domains/domain.com/public_html
sub1.domain.com => /domains/domain.com/subdomains/sub1/public_html

In my cpanel I don't have the option to put something before the public_html So everything I do is created after the public_html folder......

I am using JMS to seperate a large site I want to build. The subdomains will be apart of the main domain. I will not be using different domains or anything. IT will all be just one big site.

I just don't understand why you need such complex naming and long urls.

If your cPanel does not allows you creating an "Addon" or "Subdomain" beside the "public_html", in this case, I can just recommend you to have a "primary domain" that is not really a public domain and that you could consider it as emapty.
You could put a simple "index.html" or "htaccess" to redirect all the traffic to the correct domain (sub-directory) and also put a robot.txt that deny to index anything from this "primary domain".

In other words, use a "primary domain" that is just there to manage the cPanel and that is not used for public website.
After that, create your "Addon domain" and "subdomain" that will be a subdirectory of the "public_html" in using our naming convention.

The reason of the complex structure is explained in my previous description.
Keep each domain or subdomain specific and not share anything between the directories.
Otherwise google or other search engnine may give you penalties for duplicated content (because the content can be accessed via other domains or subdomains).

Each domain or subdomain must have their own and unique directory.
Never be a subdirectory of something else.
In your case, there is one thing that you can not forbid is the case of the primary domain that contain all the subdirectories for the domain and subdomains.
This is the reason why I mentioned that you should consider the "primary domain" as an empty website where in fact you redirect to the good one and where you put robots to avoid indexing in the search engine.