I don't know if I understand the problem. I don't do this stuff much either, so the following may not accurate.
When you set subdomain e.g.
subdomain.mydomain.com in cpanel, you could then set where it redirects to. You could set it to
mydomain.com/somefolder, or anything else.
When browser points
subdomain.mydomain.com, it will pull up the content from wherever it redirects; however, the browser's address bar will still show
Note that user will still able to access the same content by entering
So, in short if I want to make subdomain, I will just pick the subdomain's name and I'll get
subdomain.mydomain.com. No further set up necessary.
If your cpanel has different behavior, then you might want to contact your host how to accomplish what you want.