Do I need to set a package for my root domain?

Ok, I switched from shared to VPS. My main concern was getting my site up which is on an add-on domain, not my main root domain. I did that, by first creating an account and package for that domain in the WHM. But now I don't know how to set up a site on my main domain.

I can go to cpanel for my secondary domain, by going to mydomain.com/cpanel and I can ftp by going to the IP address or ftp.mydomain.com and entering the account username and password.

Those things don't work for the main domain though, with my root username and password. So do I need to do the same thing for my root domain as I did for the other domain, setup an account and package in the WHM? I don't want to mess anything up which is why I'm asking.

Thanks,

Tom