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I am creating software that allows users to either have their own custom subdomain (e.g: theirsubdomain.mydomain.com) or point a CNAME from their own domain to my website address (e.g: theirsubdomain.theirdomain.com).

I've contacted my host about this and the first subdomain option is cool. They will set-up a wilcard subdomain script for me...

The CNAME they said I can't do automatically. I will have to manually go into my account and add the domain to point to my website address otherwise apache wont now where to look for the files.

Is this common practice or is there a way around this that is automated?