In httpd.conf (which is usually located in /usr/local/apache/conf in a linux box with cpanel), you'll find a number of sections beginning with
<virtualhost. Inside each one you'll see a line for "DocumentRoot".
The path shown next to it is what the system will use to find an index file when a user tries to access the domain name itself as a url.
Also, to confirm you're dealing with the right domain, look for "ServerName" entries or even the domain name itself. After all, each individual block of text beginning with
<virtualhost contain settings specific to only one domain.
When the settings are changed, restart apache gracefully. You may want to follow the instructions at the top of the configuration file that cpanel puts in so that you can retain the changes in the configuration.
Another option which is less flexible is to try to enter user account management or even the tweak settings in the WHM, but I don't play with WHM too much since I prefer the shell.
If you don't want to play with apache configuration too much, then what you could do is create a folder where you want the documents to be located and create a symbolic link.
In linux, you'd type:
ln -s /path/to/new/folder /home/domain
where "/home/domain" is your current document root for the domain you want to change. Just make sure you set the permissions of the symbolic link and the new folder correctly or users will find their access being denied.
As always, test your setup.