How to manually add CNAME without CPanel?


I'm new to WPMUdev community. I'm trying to map a domain to one of my sub-domain site ( WP Multisite). I followed the intructions as indicated here, until the CNAME part:

My environment:
* a dedicated server with WPMS installed
* a domain name already mapped to WP root correctly

Could anyone please explain to me the following:
* how to add CNAME manually?
* What files to be edited or created on Apache side?
* Is there a way to automate this process? If not, does it mean that everytime we would like to map a domain name to one of the sub-site (sub-domain or sub-directory), a manual intervention has to be done?

Thank you for your help.