We just simply disabled all webmail access provided by Cpanel on our services
and then setup our own webmail on it's own account but with an added
"ServerAlias webmail.*" line added to Apache's httpd.conf file and our
DNS templates are setup to add a "webmail IN A xx.xx.xx.xx" line to
all domains added to the server.
The effect is our own webmail system that is not constantly overwritten by
every Cpanel update that comes out (annoying) and has the address of
http://webmail.mydomain.com where mydomain.com is the user's domain.
If you want the /webmail alias, you can do that as well by using an Include
command somewhere later in the httpd.conf file but before the Virtual host
sections and that won't be overwritten by Cpanel updates and then in your
included file put commands to override the "/webmail" alias to point to
your webmail instead of Cpanel's webmail.