I know there are a lot of threads about this and I promise I have done research for the last 2 days. I think I know what the problem is but I don't know how to fix it. This appears to be right up @aecnu 's alley...
To start I have a reseller VPS through GoDaddy running WHM/cpanel & WHMCS. I am building a multisite using subdomains to start a business website network using the spectacular plugins and themes from wpmudev.org. I have very little experience with WHM/cpanel/WHMCS.
I found a comment that you need to have the home directory to be the multisite install. The multisite domain that I currently using has the default home directory /home/username and I think I need to make it /home/username/public_html since that is where my multisite install is located.
I read that you can change this using SSH. I downloaded putty and I could login but I could not find the httpd.conf file to edit the virtual host. I've also tried to add a vhost using the include editor in WHM which was unsuccessful. I read that it might be possible to create an additional cpanel account and have one for the reseller and one for the multisite, both with dedicated IP's and proper home directories.
I believe that I have set up the domain mapping correctly in wordpress and the DNS A name. When I enter the user's domain that needs to be mapped to my subdomain I get /cgi-sys/defaultwebpage.cgi
In the future I would like to be able to sell hosting, domains, email, SSL, etc. through WHMCS but that will not be my primary source of income. I just want to get the domain mapping plugin working right now. Please help!