SquareMan

Guys I have one big problem creating independent subdomains ,
lets say my domain is , SQdomain.com , I want to have a secondary domain as separate site like Site1.SQdomain.com . I logged in to my cpanel and under the Domains section , I clicked the subdomain Icon and created that subdomain (site1.SQdomain.com) , later I've found out that this subdomain added as a subdirectory folder within my web site so the subdomain site can be accessed in both ways :
Site1.SQdomain.com and SQdomain.com/Site1/

I've checked other sites which are usin subdomains , and non of them were like that ( it's only accessable through the exact subdomain address , not by usnig slashes )

What should I do to have a real subdomain that can act as a seprate site ?
BTW I have a reseller hosting account .

Thanks