Hi,
I'm using cPanel in my server, how to prevent:

1. Creating a sub domain with its own directory cause 2 URLs creation
E.g. I have a master site like www.domain.com, then I create a slave site such as blog.domain.com with its own directory "blog". By this way, I will have 2 URLS for the slave site, they are blog.domain.com and domain.com/blog/ which it will cause a duplicate content for SEO.

2. Creating an addon domain cause 2 URLS creation
E.g I have a master site like www.domainA.com, then I create an a slave site from addon domain such as www.domainB.com. By this way, I will have 2 URLs for the slave site, they are www.domainB.com and domainB.domainA.com which it will cause a duplicate content for SEO.

Thanks before

In cPanel, you can decide the subdomain location.
Rather than to provide a subdirectory of you master website, you can provide another directory.

For example suppose that you cPanel use the following structure
master = /home/account/public_html

By default cPanel provide you a directory structure based on your "domain" public_html
but you can change it and use another directory structure.
For example

slave1 = /home/account/subdomains/slave1/public_html

I have suggested to keep the "public_html" in case where you would like to also have "confidential" directory for you slave1 subdomain. This would give you the possibility to create other directories insiide the "subdomains/slave1" that will not be public.

Up to you to organise the directory structure as you want.