Your description isn't clear:
Do you have mydomain.com and subdomain.mydomain.com?
How are you logging in? FTP/SSH/Telnet/Control Panel?
It sounds like you want to make mydomain.com look like subdomain.mydomain.com and vice-versa. If so, then you can just rename them in your home directory via FTP or Shell:
Rename mydomain.com as hold.mydomain.com
Rename subdomain.mydomain.com as mydomain.com
Rename hold.mydomain.com as subdomain.mydomain.com