Well, you have two options in cPanel, and one in WHM:

cPanel:
Parked Domain: /home/[username]/public_html/ (of main domain)
Addon Domain: /home/[username]/public_html/subfolder (of main domain)

Addon also creates a subdomain but its not required that it is used, and I'd gather you could edit the DNS zone to remove it if you didn't want it web accessible for some reason.

WHM:
Create a New account:/ /home/[username]/public_html/ (is now a main domain)