To whom it may concern… Setting up Cloudflare Registrar, C-Panel Domain and finally WP Site:
1) Do not setup the site in WP first! Wait. I you did, delete it and start over later.
1a) Register domain at Cloudflare and set up DNS Records. You need A Record – Name mysite.com – Point it to the IP of your top site.
2) Login to cpanel of your host and go to Domain > Create Domain > Name mysite.com. Set Document root to public_html …. the same as the main install
3) In C-Panel > Zone Editor…. Make sure mysite.com shows. Here you can manage records, however it should work as is.
4) Also for mail setup, you have DKIM SPF, that you need over on Cloudflare for mail record. You can have Cloudflare auto setup and then apply keys in respective records if you wish host mail server to execute as opposed to Cloudflare routing
5) Jump to WP Dashboard for Multisite go to Sites > Add New Site and fill out the fields…. save
6) Go back and edit this site and change site name to not sub site but mysite.com
Note: Cache persistently obstructed the display of my site. So for the browser CLEAR CACHE NOW!
I hope this may be of help to someone….