Domain Mapping - URGENT!!!

I have wasted 3 days now without progress. It has also caused all my subdomains to break. I even logged my problem this morning without any reply.

I wish to talk to someone in real-time as I'm out of patience!!
…….
Im still having problems setting up.

I use cloud flare and have multiple domains and wish to structure my wpmu site in the following way. Do I use the CF Ip or my host server Ip or list both?

1. primary domain = my company domain.
2. root domains = e.g blue.com, yellow.com, red.com
3. sub domains = e.g light.blue.com, dark.yellow.com, bright.red.com

Basically I cannot add the root domain as there is no option for this in 'Add new Site' section.

I noticed these options in the video but I don't see this in my setup. i.e with these option i would be able to add the root domain site/address to my wp-mu. How do I activate?

https://www.dropbox.com/s/2di249utjy2w1b5/Screenshot%202016-09-05%2011.49.02.png?dl=0