So here is the problem that has presented itself to me today.
I'm on a VPS machine with WHM / cPanel (a pain I know).
I'm in full control of both and the VPS.
Currently I have an account setup on it called xyz.
I have MU enabled and subdomains are working great.
Users can visit whatever.xyz.com and it is all working properly.
The real issue here is when enabling the Domain Mapping feature.
If a user creates a CNAME pointed to the IP (it is dedicated but visiting it goes to the WHM default page and not the blog site. To get to the blog site users must visit $IPADDRESS/~xyz)
I've been looking and trying to figure out how to make $IPADDRESS default to the /home/xyz/public_html directory and haven't had any luck.